From gss at dev.open-bio.org Mon Apr 3 19:28:37 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 3 Apr 2006 19:28:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604032328.k33NSbtR020406@dev.open-bio.org> gss Mon Apr 3 19:28:37 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools In directory dev.open-bio.org:/tmp/cvs-serv20374/src/org/semanticmoby/ref/tools Modified Files: MOBYProperties.java Log Message: Get location of properties file from smoby.properties-path system property s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools MOBYProperties.java,1.7,1.8 From gss at dev.open-bio.org Mon Apr 3 19:30:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 3 Apr 2006 19:30:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604032330.k33NUV9L020446@dev.open-bio.org> gss Mon Apr 3 19:30:31 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets In directory dev.open-bio.org:/tmp/cvs-serv20414/src/org/semanticmoby/ref/servlets Modified Files: InitServlet.java Log Message: Changes to work with changed MOBYProperties s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets InitServlet.java,1.2,1.3 From gss at dev.open-bio.org Mon Apr 3 19:33:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 3 Apr 2006 19:33:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604032333.k33NXTWr020486@dev.open-bio.org> gss Mon Apr 3 19:33:29 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv20454 Modified Files: cvstag.log Log Message: Added entry for build-2006-4a s-moby cvstag.log,1.3,1.4 From mwilkinson at dev.open-bio.org Tue Apr 4 20:00:04 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 4 Apr 2006 20:00:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604050000.k350049f023999@dev.open-bio.org> mwilkinson Tue Apr 4 20:00:03 EDT 2006 Update of /home/repository/moby/moby-live/OWL In directory dev.open-bio.org:/tmp/cvs-serv23982 Modified Files: ServiceDescription.owl ServiceDescriptions.swp Log Message: OWL-DL ontology for MOBY services. Properly formatted Service Instance RDF should classify into this ontology as a serviceDescription object. moby-live/OWL ServiceDescription.owl,1.1,1.2 ServiceDescriptions.swp,1.1,1.2 From mwilkinson at dev.open-bio.org Tue Apr 4 20:05:46 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 4 Apr 2006 20:05:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604050005.k3505kaK024076@dev.open-bio.org> mwilkinson Tue Apr 4 20:05:46 EDT 2006 Update of /home/repository/moby/moby-live/OWL In directory dev.open-bio.org:/tmp/cvs-serv24060 Modified Files: ServiceDescription.owl Log Message: making the URI resolvable from the online CVS moby-live/OWL ServiceDescription.owl,1.2,1.3 From gss at dev.open-bio.org Wed Apr 5 16:43:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 5 Apr 2006 16:43:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604052043.k35KhI5K031629@dev.open-bio.org> gss Wed Apr 5 16:43:18 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java In directory dev.open-bio.org:/tmp/cvs-serv31595/src/java Log Message: Directory /home/repository/moby/s-moby/provider/src/java added to the repository s-moby/provider/src/java - New directory From gss at dev.open-bio.org Wed Apr 5 16:43:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 5 Apr 2006 16:43:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604052043.k35KhI5o031648@dev.open-bio.org> gss Wed Apr 5 16:43:18 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java/org In directory dev.open-bio.org:/tmp/cvs-serv31595/src/java/org Log Message: Directory /home/repository/moby/s-moby/provider/src/java/org added to the repository s-moby/provider/src/java/org - New directory From gss at dev.open-bio.org Wed Apr 5 16:43:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 5 Apr 2006 16:43:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604052043.k35KhI82031665@dev.open-bio.org> gss Wed Apr 5 16:43:18 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java/org/semanticmoby In directory dev.open-bio.org:/tmp/cvs-serv31595/src/java/org/semanticmoby Log Message: Directory /home/repository/moby/s-moby/provider/src/java/org/semanticmoby added to the repository s-moby/provider/src/java/org/semanticmoby - New directory From gss at dev.open-bio.org Wed Apr 5 16:43:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 5 Apr 2006 16:43:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604052043.k35KhI5D031688@dev.open-bio.org> gss Wed Apr 5 16:43:18 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java/org/semanticmoby/provider In directory dev.open-bio.org:/tmp/cvs-serv31595/src/java/org/semanticmoby/provider Log Message: Directory /home/repository/moby/s-moby/provider/src/java/org/semanticmoby/provider added to the repository s-moby/provider/src/java/org/semanticmoby/provider - New directory From gss at dev.open-bio.org Wed Apr 5 16:43:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 5 Apr 2006 16:43:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604052043.k35KhKrM031763@dev.open-bio.org> gss Wed Apr 5 16:43:20 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/org/semanticmoby/provider In directory dev.open-bio.org:/tmp/cvs-serv31715/src/org/semanticmoby/provider Removed Files: ParamReader.java AbstractMobyServlet.java ParameterException.java Log Message: Moved Java source files to from src/ to src/java s-moby/provider/src/org/semanticmoby/provider ParamReader.java,1.1,NONE AbstractMobyServlet.java,1.1,NONE ParameterException.java,1.1,NONE From gss at dev.open-bio.org Wed Apr 5 16:43:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 5 Apr 2006 16:43:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604052043.k35KhKaO031746@dev.open-bio.org> gss Wed Apr 5 16:43:20 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java/org/semanticmoby/provider In directory dev.open-bio.org:/tmp/cvs-serv31715/src/java/org/semanticmoby/provider Added Files: ParamReader.java AbstractMobyServlet.java ParameterException.java Log Message: Moved Java source files to from src/ to src/java s-moby/provider/src/java/org/semanticmoby/provider ParamReader.java,NONE,1.1 AbstractMobyServlet.java,NONE,1.1 ParameterException.java,NONE,1.1 From senger at dev.open-bio.org Wed Apr 5 11:55:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Apr 2006 11:55:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604051555.k35FtlFR030412@dev.open-bio.org> senger Wed Apr 5 11:55:47 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv30396/src/Clients Removed Files: HelloMOBY2.java Log Message: moby-live/Java/src/Clients HelloMOBY2.java,1.1,NONE From ivanp at mmb.pcb.ub.es Wed Apr 5 10:18:24 2006 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Wed, 05 Apr 2006 16:18:24 +0200 Subject: [MOBY-guts] jMoby seems not to compile Message-ID: <4433D1B0.1000700@mmb.pcb.ub.es> Hi, Perhaps I'm committing some mistake but I think I've updated my local copy from the last version in the CVS and when I try to compile jMoby by doing "build-dev.sh all" I get the following error: compile-normal: [javac] Compiling 273 source files to /home/apache/moby-live/Java/build/classes [javac] Note: * uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] Compiling 20 source files to /home/apache/moby-live/Java/build/Clients [javac] /home/apache/moby-live/Java/src/Clients/HelloMOBY2.java:11: HelloMOBY2 is not abstract and does not override abstract method stop(org.biomoby.client.MobyRequest,int) in org.biomoby.client.MobyRequestEventHandler [javac] public class HelloMOBY2 implements MobyRequestEventHandler{ [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 1 error Best regards, -- Iv?n P?rraga Garc?a Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es http://mmb.pcb.ub.es From kawas at dev.open-bio.org Thu Apr 6 00:03:52 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 6 Apr 2006 00:03:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604060403.k3643qUZ032163@dev.open-bio.org> kawas Thu Apr 6 00:03:52 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv32130/org/biomoby/client/rdf/builder Modified Files: RDFConfigure.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder RDFConfigure.java,1.13,1.14 From gordonp at dev.open-bio.org Thu Apr 6 09:42:44 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 6 Apr 2006 09:42:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604061342.k36DgiRd000957@dev.open-bio.org> gordonp Thu Apr 6 09:42:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv924/src/Clients Added Files: HelloMOBY2.java Log Message: Updated to reflect change in MobyRequestEventHandler interface moby-live/Java/src/Clients HelloMOBY2.java,1.2,1.3 From kawas at dev.open-bio.org Thu Apr 6 18:07:38 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 6 Apr 2006 18:07:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604062207.k36M7cxu002253@dev.open-bio.org> kawas Thu Apr 6 18:07:38 EDT 2006 Update of /home/repository/moby/moby-live/OWL In directory dev.open-bio.org:/tmp/cvs-serv2222 Added Files: MOBYPredicates.owl Log Message: moby predicates moby-live/OWL MOBYPredicates.owl,NONE,1.1 From gss at dev.open-bio.org Fri Apr 7 12:42:27 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:42:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071642.k37GgRmi005939@dev.open-bio.org> gss Fri Apr 7 12:42:27 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web In directory dev.open-bio.org:/tmp/cvs-serv5908/examples/fasta-sequence/web Added Files: resourceProvider Log Message: Instance of moby:Provider to give information about the institution that provides resources s-moby/provider/examples/fasta-sequence/web resourceProvider,NONE,1.1 From gss at dev.open-bio.org Fri Apr 7 12:43:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:43:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071643.k37Ght5U005997@dev.open-bio.org> gss Fri Apr 7 12:43:55 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web In directory dev.open-bio.org:/tmp/cvs-serv5965/examples/fasta-sequence/web Modified Files: fasta-sequence.owl Log Message: Replaced providerName and providerAboutURI properties with providedBy property that refers to the resourceProvider individual s-moby/provider/examples/fasta-sequence/web fasta-sequence.owl,1.2,1.3 From gss at dev.open-bio.org Fri Apr 7 12:45:42 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:45:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071645.k37GjgpM006144@dev.open-bio.org> gss Fri Apr 7 12:45:42 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web/terms In directory dev.open-bio.org:/tmp/cvs-serv6113/examples/fasta-sequence/web/terms Added Files: owlOntology Log Message: owl:Ontology individual used to collectively document the terms in this ontology s-moby/provider/examples/fasta-sequence/web/terms owlOntology,NONE,1.1 From gss at dev.open-bio.org Fri Apr 7 12:45:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:45:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071645.k37Gjvew006185@dev.open-bio.org> gss Fri Apr 7 12:45:57 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web/terms In directory dev.open-bio.org:/tmp/cvs-serv6149/examples/fasta-sequence/web/terms Modified Files: tcNumber FastaKey FastaSequence speciesName sequenceText Log Message: Added reference to owlOntology individual s-moby/provider/examples/fasta-sequence/web/terms tcNumber,1.1,1.2 FastaKey,1.1,1.2 FastaSequence,1.1,1.2 speciesName,1.1,1.2 sequenceText,1.1,1.2 From gss at dev.open-bio.org Fri Apr 7 12:47:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:47:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071647.k37GlB3x006225@dev.open-bio.org> gss Fri Apr 7 12:47:11 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv6193/src/org/semanticmoby/api/util Modified Files: MOBY.java Log Message: Removed providerName and providerAboutURI properties; added providedBy and providesResource properties; added documentation on properties and classes s-moby/api/src/org/semanticmoby/api/util MOBY.java,1.1,1.2 From gss at dev.open-bio.org Fri Apr 7 12:51:24 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:51:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071651.k37GpOSJ006282@dev.open-bio.org> gss Fri Apr 7 12:51:24 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv6251/src/org/semanticmoby/api Added Files: MOBYProvider.java Log Message: Class to represent information about the provider of a set of MOBY resources s-moby/api/src/org/semanticmoby/api MOBYProvider.java,NONE,1.1 From gss at dev.open-bio.org Fri Apr 7 12:52:23 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:52:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071652.k37GqN0t006319@dev.open-bio.org> gss Fri Apr 7 12:52:23 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv6287/src/org/semanticmoby/api Modified Files: MOBYGraphNode.java Log Message: Added methods for setting and getting values of literal and resource properties s-moby/api/src/org/semanticmoby/api MOBYGraphNode.java,1.1,1.2 From gss at dev.open-bio.org Fri Apr 7 12:52:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:52:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071652.k37GqteW006356@dev.open-bio.org> gss Fri Apr 7 12:52:55 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv6324/src/org/semanticmoby/api Modified Files: MOBYResource.java Log Message: Removed providerName and providerAboutURI properties; added providedBy property s-moby/api/src/org/semanticmoby/api MOBYResource.java,1.1,1.2 From gss at dev.open-bio.org Fri Apr 7 12:54:08 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:54:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071654.k37Gs8Y8006396@dev.open-bio.org> gss Fri Apr 7 12:54:08 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv6364/src/org/semanticmoby/api Modified Files: Parser.java Log Message: Modified parseResource to no longer expect providerName and providerAboutURI properties, but to expect providedBy property; added parseProvider method s-moby/api/src/org/semanticmoby/api Parser.java,1.1,1.2 From lxm at dev.open-bio.org Fri Apr 7 12:59:21 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 7 Apr 2006 12:59:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071659.k37GxLlm006440@dev.open-bio.org> lxm Fri Apr 7 12:59:21 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv6406/web Log Message: Directory /home/repository/moby/s-moby/dclient/web added to the repository s-moby/dclient/web - New directory From lxm at dev.open-bio.org Fri Apr 7 13:00:17 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 7 Apr 2006 13:00:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071700.k37H0HfO006482@dev.open-bio.org> lxm Fri Apr 7 13:00:17 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv6448/WEB-INF Log Message: Directory /home/repository/moby/s-moby/dclient/web/WEB-INF added to the repository s-moby/dclient/web/WEB-INF - New directory From lxm at dev.open-bio.org Fri Apr 7 13:02:05 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 7 Apr 2006 13:02:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071702.k37H25fD006544@dev.open-bio.org> lxm Fri Apr 7 13:02:05 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv6513 Added Files: web.xml Log Message: web.xml file for discovery client web code s-moby/dclient/web/WEB-INF web.xml,NONE,1.1 From gss at dev.open-bio.org Fri Apr 7 13:47:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 13:47:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071747.k37Hle7D006776@dev.open-bio.org> gss Fri Apr 7 13:47:40 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web/terms In directory dev.open-bio.org:/tmp/cvs-serv6744/provider/examples/fasta-sequence/web/terms Modified Files: owlOntology Log Message: Fixed a typo (missing quote) s-moby/provider/examples/fasta-sequence/web/terms owlOntology,1.1,1.2 From kawas at dev.open-bio.org Tue Apr 11 08:15:40 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 08:15:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111215.k3BCFevV032631@dev.open-bio.org> kawas Tue Apr 11 08:15:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv32599/MOBY/Parser Modified Files: MobyPackage.pm Log Message: moby-live/Java/src/Perl/MOBY/Parser MobyPackage.pm,1.2,1.3 From kawas at dev.open-bio.org Tue Apr 11 08:16:04 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 08:16:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111216.k3BCG4qC032704@dev.open-bio.org> kawas Tue Apr 11 08:16:04 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv32672/MOBY/Parser Modified Files: MobyParser.pm Log Message: moby-live/Java/src/Perl/MOBY/Parser MobyParser.pm,1.5,1.6 From kawas at dev.open-bio.org Tue Apr 11 08:16:54 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 08:16:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111216.k3BCGsjk032759@dev.open-bio.org> kawas Tue Apr 11 08:16:54 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv32727/MOBY/Parser Modified Files: MobyParameter.pm Log Message: moby-live/Java/src/Perl/MOBY/Parser MobyParameter.pm,1.2,1.3 From kawas at dev.open-bio.org Tue Apr 11 10:40:28 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 10:40:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111440.k3BEeSR2000529@dev.open-bio.org> kawas Tue Apr 11 10:40:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv498/org/biomoby/client/rdf/vocabulary Added Files: DC_PROTEGE.java Log Message: DC vocab that is owl-dl moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary DC_PROTEGE.java,NONE,1.1 From kawas at dev.open-bio.org Tue Apr 11 10:43:52 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 10:43:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111443.k3BEhqNr000569@dev.open-bio.org> kawas Tue Apr 11 10:43:52 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv537/org/biomoby/shared/extended Modified Files: ServiceTypeParser.java Log Message: updated to parse RDF that contains dc_protege. moby-live/Java/src/main/org/biomoby/shared/extended ServiceTypeParser.java,1.5,1.6 From kawas at dev.open-bio.org Tue Apr 11 10:45:00 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 10:45:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111445.k3BEj0ZG000609@dev.open-bio.org> kawas Tue Apr 11 10:45:00 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv577/org/biomoby/shared/extended Modified Files: NamespaceParser.java Log Message: updated to parse RDF that contains dc_protege. moby-live/Java/src/main/org/biomoby/shared/extended NamespaceParser.java,1.5,1.6 From kawas at dev.open-bio.org Tue Apr 11 10:46:15 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 10:46:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111446.k3BEkFP3000649@dev.open-bio.org> kawas Tue Apr 11 10:46:15 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv617/org/biomoby/shared/extended Modified Files: ServiceTypeParser.java Log Message: moby-live/Java/src/main/org/biomoby/shared/extended ServiceTypeParser.java,1.6,1.7 From kawas at dev.open-bio.org Tue Apr 11 10:48:40 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 10:48:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111448.k3BEmelY000707@dev.open-bio.org> kawas Tue Apr 11 10:48:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv675/org/biomoby/shared/extended Modified Files: DataTypeParser.java Log Message: updated to parse RDF that contains dc_protege. moby-live/Java/src/main/org/biomoby/shared/extended DataTypeParser.java,1.4,1.5 From kawas at dev.open-bio.org Tue Apr 11 10:57:52 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 10:57:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111457.k3BEvqSk000747@dev.open-bio.org> kawas Tue Apr 11 10:57:52 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv715/org/biomoby/shared/extended Modified Files: ServiceInstanceParser.java Log Message: updated to parse RDF that contains dc_protege. moby-live/Java/src/main/org/biomoby/shared/extended ServiceInstanceParser.java,1.13,1.14 From kawas at dev.open-bio.org Tue Apr 11 12:08:54 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 12:08:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111608.k3BG8ssW001304@dev.open-bio.org> kawas Tue Apr 11 12:08:54 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv1272/Perl/MOBY/Datatypes Modified Files: MobyInteger.pm Log Message: documented module moby-live/Java/src/Perl/MOBY/Datatypes MobyInteger.pm,1.1,1.2 From kawas at dev.open-bio.org Tue Apr 11 12:14:16 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 12:14:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111614.k3BGEGa3001344@dev.open-bio.org> kawas Tue Apr 11 12:14:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv1312/Perl/MOBY/Datatypes Modified Files: MobyFloat.pm Log Message: documented module moby-live/Java/src/Perl/MOBY/Datatypes MobyFloat.pm,1.1,1.2 From kawas at dev.open-bio.org Tue Apr 11 12:14:23 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 12:14:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111614.k3BGENlh001381@dev.open-bio.org> kawas Tue Apr 11 12:14:23 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv1349/Perl/MOBY/Datatypes Modified Files: MobyInteger.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyInteger.pm,1.2,1.3 From kawas at dev.open-bio.org Tue Apr 11 12:18:57 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 12:18:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111618.k3BGIvjA001423@dev.open-bio.org> kawas Tue Apr 11 12:18:57 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv1391/Perl/MOBY/Datatypes Modified Files: MobyFloat.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyFloat.pm,1.2,1.3 From kawas at dev.open-bio.org Tue Apr 11 13:02:09 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 13:02:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111702.k3BH29g9002041@dev.open-bio.org> kawas Tue Apr 11 13:02:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv2009/Perl/MOBY/Datatypes Modified Files: MobyObject.pm Log Message: documented module moby-live/Java/src/Perl/MOBY/Datatypes MobyObject.pm,1.4,1.5 From kawas at dev.open-bio.org Tue Apr 11 13:13:02 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 13:13:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111713.k3BHD2iL002119@dev.open-bio.org> kawas Tue Apr 11 13:13:02 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv2087/Perl/MOBY/Datatypes Modified Files: MobyString.pm Log Message: documented module moby-live/Java/src/Perl/MOBY/Datatypes MobyString.pm,1.1,1.2 From kawas at dev.open-bio.org Tue Apr 11 13:13:33 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 13:13:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111713.k3BHDX9c002156@dev.open-bio.org> kawas Tue Apr 11 13:13:32 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv2124/Perl/MOBY/Datatypes Modified Files: MobyString.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyString.pm,1.2,1.3 From kawas at dev.open-bio.org Tue Apr 11 18:05:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 18:05:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604112205.k3BM5MjS002658@dev.open-bio.org> kawas Tue Apr 11 18:05:22 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv2625/Perl/MOBY/Parser Modified Files: MobyPackage.pm MobyJob.pm Log Message: fixed some array bugs. moby-live/Java/src/Perl/MOBY/Parser MobyPackage.pm,1.3,1.4 MobyJob.pm,1.2,1.3 From kawas at dev.open-bio.org Tue Apr 11 18:09:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 18:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604112209.k3BM9MOn002716@dev.open-bio.org> kawas Tue Apr 11 18:09:21 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv2684/Perl/MOBY/Parser Modified Files: MobyCollection.pm Log Message: modified the constructor () -> [] moby-live/Java/src/Perl/MOBY/Parser MobyCollection.pm,1.3,1.4 From kawas at dev.open-bio.org Tue Apr 11 18:46:33 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 18:46:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604112246.k3BMkXMM002798@dev.open-bio.org> kawas Tue Apr 11 18:46:33 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv2766/Perl/MOBY/Parser Modified Files: MobyJob.pm Log Message: insertDataElement was adding properly to the array moby-live/Java/src/Perl/MOBY/Parser MobyJob.pm,1.3,1.4 From gss at dev.open-bio.org Mon Apr 17 14:38:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 17 Apr 2006 14:38:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604171838.k3HIcZIl003446@dev.open-bio.org> gss Mon Apr 17 14:38:35 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv3415 Added Files: SequenceOntology.tar.gz Log Message: Initial version on conversion from OBO format file to individual based ontology s-moby/ontologies SequenceOntology.tar.gz,NONE,1.1 From gss at dev.open-bio.org Mon Apr 17 14:39:13 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 17 Apr 2006 14:39:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604171839.k3HIdDY4003500@dev.open-bio.org> gss Mon Apr 17 14:39:13 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv3469/src/java/org/semanticmoby/ontologies/util Added Files: OBOConverter.java Log Message: General purpose converter for splitting an OBO format file into an individual based ontology s-moby/ontologies/src/java/org/semanticmoby/ontologies/util OBOConverter.java,NONE,1.1 From lxm at dev.open-bio.org Tue Apr 18 17:48:37 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 18 Apr 2006 17:48:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604182148.k3ILmb2l007480@dev.open-bio.org> lxm Tue Apr 18 17:48:37 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv7449 Added Files: AbstractDiscoveryClientServlet.java DataBean.java InvocationBroker.java KeywordSearchAllServlet.java KeywordSearchServlet.java ResourceEngagementServlet.java ResourceInvestigationServlet.java ResultsDisplayServlet.java Log Message: first round of separation of functionality, client servlets group s-moby/dclient/src/org/semanticmoby/dclient AbstractDiscoveryClientServlet.java,NONE,1.1 DataBean.java,NONE,1.1 InvocationBroker.java,NONE,1.1 KeywordSearchAllServlet.java,NONE,1.1 KeywordSearchServlet.java,NONE,1.1 ResourceEngagementServlet.java,NONE,1.1 ResourceInvestigationServlet.java,NONE,1.1 ResultsDisplayServlet.java,NONE,1.1 From lxm at dev.open-bio.org Tue Apr 18 17:51:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 18 Apr 2006 17:51:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604182151.k3ILp4lO007584@dev.open-bio.org> lxm Tue Apr 18 17:51:03 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv7551 Modified Files: MOBYProperties.java StorageManager.java Added Files: DiscoveryQuery.java DiscoveryServlet.java InitServlet.java InvestigationServlet.java KeywordDiscoveryServlet.java ParamReader.java ParameterException.java Log Message: second round of separation of functionality, server servlets s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,NONE,1.1 DiscoveryServlet.java,NONE,1.1 InitServlet.java,NONE,1.1 InvestigationServlet.java,NONE,1.1 KeywordDiscoveryServlet.java,NONE,1.1 ParamReader.java,NONE,1.1 ParameterException.java,NONE,1.1 MOBYProperties.java,1.1,1.2 StorageManager.java,1.1,1.2 From gss at dev.open-bio.org Tue Apr 18 19:33:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 18 Apr 2006 19:33:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604182333.k3INXelr007775@dev.open-bio.org> gss Tue Apr 18 19:33:40 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv7742/src/java/org/semanticmoby/ontologies/util Modified Files: OBOConverter.java Log Message: Create and reference an owl:Ontology individual; write Term individuals to termIndividuals subdirectory; copy input file to output directory s-moby/ontologies/src/java/org/semanticmoby/ontologies/util OBOConverter.java,1.1,1.2 From gss at dev.open-bio.org Tue Apr 18 19:36:33 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 18 Apr 2006 19:36:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604182336.k3INaXUD007835@dev.open-bio.org> gss Tue Apr 18 19:36:33 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv7803/ontologies Modified Files: SequenceOntology.tar.gz Log Message: Created and reference an owl:Ontology individual; Term individuals now in termIndividuals subdirectory; added so.obo input file to output directory s-moby/ontologies SequenceOntology.tar.gz,1.1,1.2 From kawas at dev.open-bio.org Wed Apr 19 14:46:07 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Apr 2006 14:46:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604191846.k3JIk7ke009893@dev.open-bio.org> kawas Wed Apr 19 14:46:06 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv9861/MOBY-S_API Modified Files: InputMessage.html Log Message: incorrect link for seconary inputs. moby-live/Docs/MOBY-S_API InputMessage.html,1.4,1.5 From kawas at dev.open-bio.org Wed Apr 19 17:34:46 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Apr 2006 17:34:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604192134.k3JLYk92010677@dev.open-bio.org> kawas Wed Apr 19 17:34:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv10601/workflows Modified Files: 1 - workflow.xml 2 - blastDragonDbWorkflow.xml 4 - characterizeGeneticElement.xml 5 - BlastQueryAgainstAraProteinsE13.xml readme.txt 8 - hmm dragon workflow.xml 3 - cos_fixedInput.xml 6 - compareKeywordAndSimilarity.xml 1 - workflowInput.xml 7 - compareKeywordAndSimilarityAndPhytoprot_count.xml Added Files: 12 - TAIR_UBCFullWorkflow.xml 14 - BiomobyAndEMBOSSInteroperability.xml 13 - TAIR_UBCFullWorkflow-CollectionAsSimples.xml 16 - StringManipulationWorkflow.xml 15 - BiomobyAndEMBOSSInteroperability.xml 10 - GeneInfo workflow.xml 11 - KeggID2GeneInformation.xml Log Message: new workflows that work with the latest taverna plugin. most should be backwards compatible except for new ports that are used. moby-live/Java/docs/taverna/workflows 12 - TAIR_UBCFullWorkflow.xml,NONE,1.1 14 - BiomobyAndEMBOSSInteroperability.xml,NONE,1.1 13 - TAIR_UBCFullWorkflow-CollectionAsSimples.xml,NONE,1.1 16 - StringManipulationWorkflow.xml,NONE,1.1 15 - BiomobyAndEMBOSSInteroperability.xml,NONE,1.1 10 - GeneInfo workflow.xml,NONE,1.1 11 - KeggID2GeneInformation.xml,NONE,1.1 1 - workflow.xml,1.2,1.3 2 - blastDragonDbWorkflow.xml,1.2,1.3 4 - characterizeGeneticElement.xml,1.2,1.3 5 - BlastQueryAgainstAraProteinsE13.xml,1.2,1.3 readme.txt,1.1,1.2 8 - hmm dragon workflow.xml,1.1,1.2 3 - cos_fixedInput.xml,1.2,1.3 6 - compareKeywordAndSimilarity.xml,1.2,1.3 1 - workflowInput.xml,1.2,1.3 7 - compareKeywordAndSimilarityAndPhytoprot_count.xml,1.2,1.3 From kawas at dev.open-bio.org Wed Apr 19 17:52:02 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Apr 2006 17:52:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604192152.k3JLq2sB010856@dev.open-bio.org> kawas Wed Apr 19 17:52:02 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv10807/guide Modified Files: completeDnasequence.png serviceContextClick.png index.html workflowComplete.png objectTooltip.png results.png dnaConnectedMelting.png serviceTooltip.png addDNAtoModel.png tutorialWorkflowInput.xml contextObjectDetails.png workflows.html dnasequence.png objectContextMenu.png tutorialWorkflow.xml serviceDescription.png addingMelting.png msdAddToWorkflow.png Added Files: mobyservicediscovery.png email.png Log Message: updated guide for taverna 1.3.2-rc1 moby-live/Java/docs/taverna/guide mobyservicediscovery.png,NONE,1.1 email.png,NONE,1.1 completeDnasequence.png,1.1,1.2 serviceContextClick.png,1.1,1.2 index.html,1.4,1.5 workflowComplete.png,1.1,1.2 objectTooltip.png,1.1,1.2 results.png,1.1,1.2 dnaConnectedMelting.png,1.1,1.2 serviceTooltip.png,1.1,1.2 addDNAtoModel.png,1.1,1.2 tutorialWorkflowInput.xml,1.1,1.2 contextObjectDetails.png,1.1,1.2 workflows.html,1.3,1.4 dnasequence.png,1.1,1.2 objectContextMenu.png,1.1,1.2 tutorialWorkflow.xml,1.1,1.2 serviceDescription.png,1.1,1.2 addingMelting.png,1.1,1.2 msdAddToWorkflow.png,1.1,1.2 From gss at dev.open-bio.org Wed Apr 19 19:46:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 19 Apr 2006 19:46:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604192346.k3JNkVuZ011080@dev.open-bio.org> gss Wed Apr 19 19:46:31 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv11049/src/java/org/semanticmoby/ontologies/util Added Files: RDFFormatter.java Log Message: A class to help generate readable RDF/XML s-moby/ontologies/src/java/org/semanticmoby/ontologies/util RDFFormatter.java,NONE,1.1 From gss at dev.open-bio.org Wed Apr 19 19:46:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 19 Apr 2006 19:46:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604192346.k3JNkwle011117@dev.open-bio.org> gss Wed Apr 19 19:46:58 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv11085/src/java/org/semanticmoby/ontologies/util Modified Files: OBOConverter.java Log Message: Changed to use the RDFFormatter helper class s-moby/ontologies/src/java/org/semanticmoby/ontologies/util OBOConverter.java,1.2,1.3 From kawas at dev.open-bio.org Wed Apr 19 20:07:55 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Apr 2006 20:07:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604200007.k3K07t6s011180@dev.open-bio.org> kawas Wed Apr 19 20:07:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv11147/guide Modified Files: index.html Log Message: moby-live/Java/docs/taverna/guide index.html,1.5,1.6 From kawas at dev.open-bio.org Wed Apr 19 20:09:36 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Apr 2006 20:09:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604200009.k3K09akg011220@dev.open-bio.org> kawas Wed Apr 19 20:09:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv11188/guide Modified Files: index.html Log Message: fixed another link moby-live/Java/docs/taverna/guide index.html,1.6,1.7 From kawas at dev.open-bio.org Thu Apr 20 11:05:16 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:05:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201505.k3KF5G7P013346@dev.open-bio.org> kawas Thu Apr 20 11:05:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv13314/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: dc -> dc_protege moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.16,1.17 From kawas at dev.open-bio.org Thu Apr 20 11:05:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:05:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201505.k3KF5hNX013400@dev.open-bio.org> kawas Thu Apr 20 11:05:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img In directory dev.open-bio.org:/tmp/cvs-serv13369/org/biomoby/client/ui/graphical/applets/img Added Files: blurredMoby.png Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img blurredMoby.png,NONE,1.1 From kawas at dev.open-bio.org Thu Apr 20 11:07:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:07:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201507.k3KF7M9e013528@dev.open-bio.org> kawas Thu Apr 20 11:07:22 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared In directory dev.open-bio.org:/tmp/cvs-serv13497/org/biomoby/client/ui/graphical/applets/shared Added Files: ThreadWorker.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared ThreadWorker.java,NONE,1.1 From kawas at dev.open-bio.org Thu Apr 20 11:07:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:07:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201507.k3KF7hfn013631@dev.open-bio.org> kawas Thu Apr 20 11:07:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util In directory dev.open-bio.org:/tmp/cvs-serv13598/org/biomoby/client/ui/graphical/applets/util Modified Files: REGEXP.java Added Files: Authenticator.java LoadRDFTrees.java RDFProgressMonitor.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util Authenticator.java,NONE,1.1 LoadRDFTrees.java,NONE,1.1 RDFProgressMonitor.java,NONE,1.1 REGEXP.java,1.2,1.3 From kawas at dev.open-bio.org Thu Apr 20 11:07:56 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:07:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201507.k3KF7uVp013689@dev.open-bio.org> kawas Thu Apr 20 11:07:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool In directory dev.open-bio.org:/tmp/cvs-serv13656/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool Modified Files: NamespaceTree.java ServiceTypeTree.java Added Files: ServiceInstanceEditorWindow.java MobyDataTreeMouseListener.java SIMain.java PopUpWindow.java ServiceTypeMouseListener.java NamespaceKeyListener.java PrimaryInputOutputTableRender.java RegistrySelectWindow.java RegisterFormattedTextWindow.java NamespaceMouseListener.java ServiceTypeKeyListener.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool ServiceInstanceEditorWindow.java,NONE,1.1 MobyDataTreeMouseListener.java,NONE,1.1 SIMain.java,NONE,1.1 PopUpWindow.java,NONE,1.1 ServiceTypeMouseListener.java,NONE,1.1 NamespaceKeyListener.java,NONE,1.1 PrimaryInputOutputTableRender.java,NONE,1.1 RegistrySelectWindow.java,NONE,1.1 RegisterFormattedTextWindow.java,NONE,1.1 NamespaceMouseListener.java,NONE,1.1 ServiceTypeKeyListener.java,NONE,1.1 NamespaceTree.java,1.2,1.3 ServiceTypeTree.java,1.2,1.3 From kawas at dev.open-bio.org Thu Apr 20 11:08:18 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:08:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201508.k3KF8IkP013746@dev.open-bio.org> kawas Thu Apr 20 11:08:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv13715/org/biomoby/client/ui/graphical/servlet/forms Added Files: RDFAgentValidator.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms RDFAgentValidator.java,NONE,1.1 From kawas at dev.open-bio.org Thu Apr 20 11:08:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:08:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201508.k3KF8g5m013804@dev.open-bio.org> kawas Thu Apr 20 11:08:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources In directory dev.open-bio.org:/tmp/cvs-serv13772/org/biomoby/client/ui/graphical/servlet/jresources Modified Files: RESOURCE.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.15,1.16 From kawas at dev.open-bio.org Thu Apr 20 11:10:06 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:10:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201510.k3KFA6NQ013879@dev.open-bio.org> kawas Thu Apr 20 11:10:06 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central In directory dev.open-bio.org:/tmp/cvs-serv13848/org/biomoby/registry/Central Added Files: CentralImpl.java Log Message: moby-live/Java/src/main/org/biomoby/registry/Central CentralImpl.java,NONE,1.1 From kawas at dev.open-bio.org Thu Apr 20 11:10:14 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:10:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201510.k3KFAEmn013933@dev.open-bio.org> kawas Thu Apr 20 11:10:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central In directory dev.open-bio.org:/tmp/cvs-serv13902/org/biomoby/registry/Central Added Files: RegistryImpl.java Log Message: moby-live/Java/src/main/org/biomoby/registry/Central RegistryImpl.java,NONE,1.1 From kawas at dev.open-bio.org Thu Apr 20 11:10:44 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:10:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201510.k3KFAiHJ014010@dev.open-bio.org> kawas Thu Apr 20 11:10:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/properties In directory dev.open-bio.org:/tmp/cvs-serv13978/org/biomoby/registry/properties Modified Files: WindowsNT.java Log Message: moby-live/Java/src/main/org/biomoby/registry/properties WindowsNT.java,1.1,1.2 From kawas at dev.open-bio.org Thu Apr 20 11:15:49 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:15:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201515.k3KFFnLi014164@dev.open-bio.org> kawas Thu Apr 20 11:15:49 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central In directory dev.open-bio.org:/tmp/cvs-serv14131/org/biomoby/registry/Central Modified Files: CentralImpl.java Log Message: moby-live/Java/src/main/org/biomoby/registry/Central CentralImpl.java,1.1,1.2 From kawas at dev.open-bio.org Thu Apr 20 11:17:28 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:17:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201517.k3KFHSph014228@dev.open-bio.org> kawas Thu Apr 20 11:17:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central In directory dev.open-bio.org:/tmp/cvs-serv14196/org/biomoby/registry/Central Modified Files: RegistryImpl.java Log Message: moby-live/Java/src/main/org/biomoby/registry/Central RegistryImpl.java,1.1,1.2 From kawas at dev.open-bio.org Thu Apr 20 11:17:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:17:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201517.k3KFHhi9014265@dev.open-bio.org> kawas Thu Apr 20 11:17:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central In directory dev.open-bio.org:/tmp/cvs-serv14233/org/biomoby/registry/Central Modified Files: RegistryImpl.java Log Message: moby-live/Java/src/main/org/biomoby/registry/Central RegistryImpl.java,1.2,1.3 From kawas at dev.open-bio.org Fri Apr 21 12:31:30 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Apr 2006 12:31:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604211631.k3LGVUfL022475@dev.open-bio.org> kawas Fri Apr 21 12:31:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv22442/Java/docs/taverna/guide Modified Files: workflows.html Log Message: fixed the layout so that it is more pleasing to the eye moby-live/Java/docs/taverna/guide workflows.html,1.4,1.5 From kawas at dev.open-bio.org Fri Apr 21 13:04:07 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Apr 2006 13:04:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604211704.k3LH47U5022567@dev.open-bio.org> kawas Fri Apr 21 13:04:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv22535/Java/docs/taverna/guide Modified Files: index.html Log Message: new question added some typos fixed moby-live/Java/docs/taverna/guide index.html,1.7,1.8 From gss at dev.open-bio.org Fri Apr 21 16:46:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 21 Apr 2006 16:46:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604212046.k3LKkpcr026624@dev.open-bio.org> gss Fri Apr 21 16:46:51 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv26591/src/java/org/semanticmoby/ontologies/util Modified Files: OBOConverter.java Log Message: Moved much of the functionality from main() into constructor and convert() method, in prepration for making a web deployment of this class s-moby/ontologies/src/java/org/semanticmoby/ontologies/util OBOConverter.java,1.3,1.4 From kawas at dev.open-bio.org Sun Apr 23 19:49:35 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sun, 23 Apr 2006 19:49:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604232349.k3NNnZbG016820@dev.open-bio.org> kawas Sun Apr 23 19:49:35 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool In directory dev.open-bio.org:/tmp/cvs-serv16788/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool Modified Files: ServiceInstanceEditorWindow.java Log Message: commented out setMaximum/MinimumSize moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool ServiceInstanceEditorWindow.java,1.1,1.2 From kawas at dev.open-bio.org Mon Apr 24 09:11:14 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 24 Apr 2006 09:11:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604241311.k3ODBESf025815@dev.open-bio.org> kawas Mon Apr 24 09:11:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool In directory dev.open-bio.org:/tmp/cvs-serv25783/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool Modified Files: ServiceInstanceEditorWindow.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool ServiceInstanceEditorWindow.java,1.2,1.3 From kawas at dev.open-bio.org Mon Apr 24 10:20:30 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 24 Apr 2006 10:20:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604241420.k3OEKU43026021@dev.open-bio.org> kawas Mon Apr 24 10:20:29 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool In directory dev.open-bio.org:/tmp/cvs-serv25989 Modified Files: RegisterFormattedTextWindow.java Log Message: jvm 1.4 compat moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool RegisterFormattedTextWindow.java,1.1,1.2 From kawas at dev.open-bio.org Mon Apr 24 10:21:13 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 24 Apr 2006 10:21:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604241421.k3OELDSC026082@dev.open-bio.org> kawas Mon Apr 24 10:21:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util In directory dev.open-bio.org:/tmp/cvs-serv26050 Modified Files: RDFProgressMonitor.java Log Message: jvm 1.4 compat moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util RDFProgressMonitor.java,1.1,1.2 From mwilkinson at dev.open-bio.org Mon Apr 24 14:06:36 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Mon, 24 Apr 2006 14:06:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604241806.k3OI6aP1026540@dev.open-bio.org> mwilkinson Mon Apr 24 14:06:36 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv26524 Modified Files: ConstructingYourService.html Log Message: services require output article name - added this to the example moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.6,1.7 From lxm at dev.open-bio.org Tue Apr 25 13:48:38 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Apr 2006 13:48:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604251748.k3PHmcZK029021@dev.open-bio.org> lxm Tue Apr 25 13:48:38 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv28987/developer Log Message: Directory /home/repository/moby/s-moby/dclient/web/developer added to the repository s-moby/dclient/web/developer - New directory From lxm at dev.open-bio.org Tue Apr 25 13:50:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Apr 2006 13:50:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604251750.k3PHoMqP029102@dev.open-bio.org> lxm Tue Apr 25 13:50:22 EDT 2006 Update of /home/repository/moby/s-moby/dclient In directory dev.open-bio.org:/tmp/cvs-serv29071 Added Files: build.xml Log Message: jsp pages for the discovery client functionality s-moby/dclient build.xml,NONE,1.1 From lxm at dev.open-bio.org Tue Apr 25 13:50:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Apr 2006 13:50:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604251750.k3PHoMGc029116@dev.open-bio.org> lxm Tue Apr 25 13:50:22 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv29071/web Added Files: about.jsp contact.jsp data-header.jsp error.jsp footer.jsp header.jsp help.jsp index.jsp search-results.jsp sql-query.jsp Log Message: jsp pages for the discovery client functionality s-moby/dclient/web about.jsp,NONE,1.1 contact.jsp,NONE,1.1 data-header.jsp,NONE,1.1 error.jsp,NONE,1.1 footer.jsp,NONE,1.1 header.jsp,NONE,1.1 help.jsp,NONE,1.1 index.jsp,NONE,1.1 search-results.jsp,NONE,1.1 sql-query.jsp,NONE,1.1 From lxm at dev.open-bio.org Tue Apr 25 13:50:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Apr 2006 13:50:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604251750.k3PHoMTA029134@dev.open-bio.org> lxm Tue Apr 25 13:50:22 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv29071/web/developer Added Files: acknowledge.jsp dev-tools.jsp index.jsp search.jsp suggest.jsp tech-overview.jsp Log Message: jsp pages for the discovery client functionality s-moby/dclient/web/developer acknowledge.jsp,NONE,1.1 dev-tools.jsp,NONE,1.1 index.jsp,NONE,1.1 search.jsp,NONE,1.1 suggest.jsp,NONE,1.1 tech-overview.jsp,NONE,1.1 From kawas at dev.open-bio.org Tue Apr 25 15:25:36 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 15:25:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604251925.k3PJPa3c029401@dev.open-bio.org> kawas Tue Apr 25 15:25:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool In directory dev.open-bio.org:/tmp/cvs-serv29369/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool Modified Files: SIMain.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool SIMain.java,1.1,1.2 From mwilkinson at dev.open-bio.org Tue Apr 25 17:13:41 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 25 Apr 2006 17:13:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252113.k3PLDfJ5029643@dev.open-bio.org> mwilkinson Tue Apr 25 17:13:41 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv29608/MOBY/Client Modified Files: CollectionArticle.pm SecondaryArticle.pm SimpleArticle.pm Log Message: fixing namespace problem with creating articles from XML DOM and updating documentation. moby-live/Perl/MOBY/Client CollectionArticle.pm,1.12,1.13 SecondaryArticle.pm,1.8,1.9 SimpleArticle.pm,1.9,1.10 From mwilkinson at dev.open-bio.org Tue Apr 25 17:13:41 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 25 Apr 2006 17:13:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252113.k3PLDfIt029624@dev.open-bio.org> mwilkinson Tue Apr 25 17:13:41 EDT 2006 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv29608 Modified Files: index.html Log Message: fixing namespace problem with creating articles from XML DOM and updating documentation. moby-live/Perl index.html,1.5,1.6 From mwilkinson at dev.open-bio.org Tue Apr 25 17:30:27 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 25 Apr 2006 17:30:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252130.k3PLURlF029810@dev.open-bio.org> mwilkinson Tue Apr 25 17:30:27 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv29792/MOBY/Client Modified Files: CollectionArticle.pm SecondaryArticle.pm SimpleArticle.pm Log Message: fixing namespace problem with creating articles from XML DOM and updating documentation. moby-live/Perl/MOBY/Client CollectionArticle.pm,1.13,1.14 SecondaryArticle.pm,1.9,1.10 SimpleArticle.pm,1.10,1.11 From mwilkinson at dev.open-bio.org Tue Apr 25 17:37:19 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 25 Apr 2006 17:37:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252137.k3PLbJXp029885@dev.open-bio.org> mwilkinson Tue Apr 25 17:37:19 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv29869/MOBY/Client Modified Files: SecondaryArticle.pm Log Message: fixing namespace problem with creating articles from XML DOM and updating documentation. moby-live/Perl/MOBY/Client SecondaryArticle.pm,1.10,1.11 From kawas at dev.open-bio.org Tue Apr 25 17:48:04 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 17:48:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252148.k3PLm4mk029943@dev.open-bio.org> kawas Tue Apr 25 17:48:04 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv29911/org/biomoby/client/rdf/builder Modified Files: RDFConfigure.java Log Message: convert to dc-protege moby-live/Java/src/main/org/biomoby/client/rdf/builder RDFConfigure.java,1.14,1.15 From kawas at dev.open-bio.org Tue Apr 25 17:48:47 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 17:48:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252148.k3PLmlUx029980@dev.open-bio.org> kawas Tue Apr 25 17:48:47 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv29948/org/biomoby/client/rdf/builder Modified Files: RDFConfigure.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder RDFConfigure.java,1.15,1.16 From mwilkinson at dev.open-bio.org Tue Apr 25 18:03:50 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 25 Apr 2006 18:03:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252203.k3PM3ogT030058@dev.open-bio.org> mwilkinson Tue Apr 25 18:03:50 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv30042/MOBY/Client Modified Files: SimpleArticle.pm Log Message: fixing namespace problem with creating articles from XML DOM and updating documentation. moby-live/Perl/MOBY/Client SimpleArticle.pm,1.11,1.12 From kawas at dev.open-bio.org Tue Apr 25 18:04:27 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 18:04:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252204.k3PM4R7v030116@dev.open-bio.org> kawas Tue Apr 25 18:04:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv30084/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.17,1.18 From kawas at dev.open-bio.org Tue Apr 25 18:30:12 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 18:30:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252230.k3PMUCNW030199@dev.open-bio.org> kawas Tue Apr 25 18:30:12 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv30167/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.18,1.19 From kawas at dev.open-bio.org Tue Apr 25 18:43:02 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 18:43:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252243.k3PMh27h030280@dev.open-bio.org> kawas Tue Apr 25 18:43:01 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv30248/org/biomoby/client/rdf/builder Modified Files: RDFConfigure.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder RDFConfigure.java,1.16,1.17 From kawas at dev.open-bio.org Tue Apr 25 19:49:07 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 19:49:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252349.k3PNn77b030368@dev.open-bio.org> kawas Tue Apr 25 19:49:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv30334/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java RDFConfigure.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.19,1.20 RDFConfigure.java,1.17,1.18 From kawas at dev.open-bio.org Tue Apr 25 19:49:45 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 19:49:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252349.k3PNnjwp030441@dev.open-bio.org> kawas Tue Apr 25 19:49:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv30409/org/biomoby/client/ui/graphical/servlet/lsid/authority Modified Files: LSIDDataLookup.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority LSIDDataLookup.java,1.8,1.9 From senger at dev.open-bio.org Tue Apr 25 20:57:23 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 25 Apr 2006 20:57:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604260057.k3Q0vNda030706@dev.open-bio.org> senger Tue Apr 25 20:57:23 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv30688 Modified Files: ChangeLog Dashboard-NOTES.txt index.html Added Files: PMoses-NOTES.txt Log Message: moby-live/Java/docs PMoses-NOTES.txt,NONE,1.1 ChangeLog,1.62,1.63 Dashboard-NOTES.txt,1.8,1.9 index.html,1.21,1.22 From mwilkinson at dev.open-bio.org Wed Apr 26 08:16:18 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 08:16:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261216.k3QCGI0S032259@dev.open-bio.org> mwilkinson Wed Apr 26 08:16:18 EDT 2006 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv32243 Removed Files: index.html Log Message: index is now auto generated during the perl Makefile.PL moby-live/Perl index.html,1.6,NONE From mwilkinson at dev.open-bio.org Wed Apr 26 11:16:07 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 11:16:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261516.k3QFG7Lu000342@dev.open-bio.org> mwilkinson Wed Apr 26 11:16:07 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv326/MOBY Modified Files: CommonSubs.pm Log Message: TOTAL re-vamp of the CommonSubs code. New paradigm for building Perl services using a more OO approach. Still don't have objects to represent MOBY objects, but there are objects to represent Simple, Collection, and Secondary articles. Hello from the TIGR MOBY workshop\! moby-live/Perl/MOBY CommonSubs.pm,1.73,1.74 From mwilkinson at dev.open-bio.org Wed Apr 26 11:48:53 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 11:48:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261548.k3QFmr3P000647@dev.open-bio.org> mwilkinson Wed Apr 26 11:48:53 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv631/MOBY Modified Files: CommonSubs.pm Log Message: fixed typos in the example service moby-live/Perl/MOBY CommonSubs.pm,1.74,1.75 From mwilkinson at dev.open-bio.org Wed Apr 26 12:18:52 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 12:18:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261618.k3QGIq9s000805@dev.open-bio.org> mwilkinson Wed Apr 26 12:18:52 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv789/MOBY Modified Files: CommonSubs.pm Log Message: fixed typos in the example service moby-live/Perl/MOBY CommonSubs.pm,1.75,1.76 From mwilkinson at dev.open-bio.org Wed Apr 26 13:14:57 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 13:14:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261714.k3QHEvwq000999@dev.open-bio.org> mwilkinson Wed Apr 26 13:14:57 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv983/scripts/Services Modified Files: LocalServices.pm Log Message: fixed typos in the example service moby-live/Perl/scripts/Services LocalServices.pm,1.65,1.66 From mwilkinson at dev.open-bio.org Wed Apr 26 13:18:10 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 13:18:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261718.k3QHIAD0001038@dev.open-bio.org> mwilkinson Wed Apr 26 13:18:10 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv1022/scripts/Services Modified Files: LocalServices.pm Log Message: fixed typos in the example service moby-live/Perl/scripts/Services LocalServices.pm,1.66,1.67 From mwilkinson at dev.open-bio.org Wed Apr 26 13:20:57 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 13:20:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261720.k3QHKv9h001075@dev.open-bio.org> mwilkinson Wed Apr 26 13:20:57 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv1059/scripts/Services Modified Files: LocalServices.pm Log Message: fixed typos in the example service moby-live/Perl/scripts/Services LocalServices.pm,1.67,1.68 From mwilkinson at dev.open-bio.org Wed Apr 26 13:47:33 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 13:47:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261747.k3QHlXW5001192@dev.open-bio.org> mwilkinson Wed Apr 26 13:47:33 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv1176/Docs/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: updating the docs for creating your service moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.7,1.8 From mwilkinson at dev.open-bio.org Wed Apr 26 14:11:11 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 14:11:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261811.k3QIBBRG001270@dev.open-bio.org> mwilkinson Wed Apr 26 14:11:11 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv1253/MOBY/Client Modified Files: CollectionArticle.pm SimpleArticle.pm Log Message: complete the object by extracting the raw XML from the DOM so that it is easily accessible as per the objects API moby-live/Perl/MOBY/Client CollectionArticle.pm,1.14,1.15 SimpleArticle.pm,1.12,1.13 From mwilkinson at dev.open-bio.org Wed Apr 26 15:58:44 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 15:58:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261958.k3QJwiJ4001483@dev.open-bio.org> mwilkinson Wed Apr 26 15:58:44 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv1467/MOBY Modified Files: CommonSubs.pm Log Message: fixing docs in CommonSubs moby-live/Perl/MOBY CommonSubs.pm,1.76,1.77 From mwilkinson at dev.open-bio.org Wed Apr 26 16:17:55 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 16:17:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604262017.k3QKHtH3001565@dev.open-bio.org> mwilkinson Wed Apr 26 16:17:55 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv1549/MOBY Modified Files: CommonSubs.pm Log Message: fixing docs in CommonSubs moby-live/Perl/MOBY CommonSubs.pm,1.77,1.78 From mwilkinson at dev.open-bio.org Thu Apr 27 06:39:23 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 06:39:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271039.k3RAdNnw003868@dev.open-bio.org> mwilkinson Thu Apr 27 06:39:22 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv3852/Perl/MOBY Modified Files: CommonSubs.pm Log Message: changed the CommonSubs input parser one more time to make it a hash of hashes. Inputs are accessible by their articleName. We are DEFINITELY no longer backwards compatible with the old API. moby-live/Perl/MOBY CommonSubs.pm,1.78,1.79 From mwilkinson at dev.open-bio.org Thu Apr 27 06:40:06 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 06:40:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271040.k3RAe6jV003905@dev.open-bio.org> mwilkinson Thu Apr 27 06:40:06 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv3889/Docs/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: updating the docs for the new CommonSubs moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.8,1.9 From mwilkinson at dev.open-bio.org Thu Apr 27 06:52:43 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 06:52:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271052.k3RAqhY6003978@dev.open-bio.org> mwilkinson Thu Apr 27 06:52:43 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv3962/Docs/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: updating docs with a better paradigm moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.9,1.10 From mwilkinson at dev.open-bio.org Thu Apr 27 06:55:03 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 06:55:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271055.k3RAt3dH004015@dev.open-bio.org> mwilkinson Thu Apr 27 06:55:03 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv3999/Perl/MOBY Modified Files: CommonSubs.pm Log Message: updating docs with a better paradigm moby-live/Perl/MOBY CommonSubs.pm,1.79,1.80 From mwilkinson at dev.open-bio.org Thu Apr 27 09:34:02 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 09:34:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271334.k3RDY2cK004200@dev.open-bio.org> mwilkinson Thu Apr 27 09:34:02 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv4184 Modified Files: LocalServices.pm Log Message: updated sample LocalServices file with the new service code paradigm moby-live/Perl/scripts/Services LocalServices.pm,1.68,1.69 From mwilkinson at dev.open-bio.org Thu Apr 27 09:34:46 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 09:34:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271334.k3RDYksG004237@dev.open-bio.org> mwilkinson Thu Apr 27 09:34:46 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv4221 Modified Files: Services.cgi Log Message: sample dispatcher now has only one service in LocalServices.pm moby-live/Perl/scripts Services.cgi,1.5,1.6 From mwilkinson at dev.open-bio.org Thu Apr 27 10:14:25 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 10:14:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271414.k3REEPIW004596@dev.open-bio.org> mwilkinson Thu Apr 27 10:14:25 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv4580/Services Modified Files: LocalServices.pm Log Message: added a scaffold example of a service that returns collections moby-live/Perl/scripts/Services LocalServices.pm,1.69,1.70 From mwilkinson at dev.open-bio.org Thu Apr 27 10:29:43 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 10:29:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271429.k3REThAP004635@dev.open-bio.org> mwilkinson Thu Apr 27 10:29:43 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv4619 Modified Files: LocalServices.pm Log Message: added a scaffold example of a service that returns collections moby-live/Perl/scripts/Services LocalServices.pm,1.70,1.71 From mwilkinson at dev.open-bio.org Thu Apr 27 10:31:32 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 10:31:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271431.k3REVWvV004714@dev.open-bio.org> mwilkinson Thu Apr 27 10:31:32 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv4698 Modified Files: CommonSubs.pm Log Message: added an example of a service that returns collections moby-live/Perl/MOBY CommonSubs.pm,1.80,1.81 From mwilkinson at dev.open-bio.org Thu Apr 27 10:33:29 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 10:33:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271433.k3REXTAi004793@dev.open-bio.org> mwilkinson Thu Apr 27 10:33:29 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv4777 Modified Files: ConstructingYourService.html Log Message: added a collection service example moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.10,1.11 From kawas at dev.open-bio.org Thu Apr 27 10:47:37 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 27 Apr 2006 10:47:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271447.k3RElb4A005157@dev.open-bio.org> kawas Thu Apr 27 10:47:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv5122/org/biomoby/shared/extended Modified Files: NamespaceParser.java DataTypeParser.java ServiceInstanceParser.java ServiceTypeParser.java Log Message: updated the RDF and its generators so that nodes in the rdf use URIs and LSIDs are not contained as a property, dublincore identifier. Parsers have been modified so that they can handle this RDF. moby-live/Java/src/main/org/biomoby/shared/extended NamespaceParser.java,1.6,1.7 DataTypeParser.java,1.5,1.6 ServiceInstanceParser.java,1.14,1.15 ServiceTypeParser.java,1.7,1.8 From kawas at dev.open-bio.org Thu Apr 27 10:47:37 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 27 Apr 2006 10:47:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271447.k3RElbXa005173@dev.open-bio.org> kawas Thu Apr 27 10:47:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv5122/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java RDFConfigure.java Log Message: updated the RDF and its generators so that nodes in the rdf use URIs and LSIDs are not contained as a property, dublincore identifier. Parsers have been modified so that they can handle this RDF. moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.20,1.21 RDFConfigure.java,1.18,1.19 From kawas at dev.open-bio.org Thu Apr 27 10:47:37 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 27 Apr 2006 10:47:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271447.k3RElbiC005214@dev.open-bio.org> kawas Thu Apr 27 10:47:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources In directory dev.open-bio.org:/tmp/cvs-serv5122/org/biomoby/client/ui/graphical/servlet/jresources Modified Files: RESOURCE.java Log Message: updated the RDF and its generators so that nodes in the rdf use URIs and LSIDs are not contained as a property, dublincore identifier. Parsers have been modified so that they can handle this RDF. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.16,1.17 From kawas at dev.open-bio.org Thu Apr 27 10:47:37 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 27 Apr 2006 10:47:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271447.k3RElbXQ005229@dev.open-bio.org> kawas Thu Apr 27 10:47:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv5122/org/biomoby/client/rdf/vocabulary Modified Files: DC_PROTEGE.java Log Message: updated the RDF and its generators so that nodes in the rdf use URIs and LSIDs are not contained as a property, dublincore identifier. Parsers have been modified so that they can handle this RDF. moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary DC_PROTEGE.java,1.1,1.2 From kawas at dev.open-bio.org Thu Apr 27 10:47:37 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 27 Apr 2006 10:47:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271447.k3RElben005193@dev.open-bio.org> kawas Thu Apr 27 10:47:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv5122/org/biomoby/client/ui/graphical/servlet/lsid/authority Modified Files: LSIDAuthorityMetaData.java LSIDDataLookup.java Log Message: updated the RDF and its generators so that nodes in the rdf use URIs and LSIDs are not contained as a property, dublincore identifier. Parsers have been modified so that they can handle this RDF. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority LSIDAuthorityMetaData.java,1.6,1.7 LSIDDataLookup.java,1.9,1.10 From mwilkinson at dev.open-bio.org Thu Apr 27 10:56:05 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 10:56:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271456.k3REu5SA005311@dev.open-bio.org> mwilkinson Thu Apr 27 10:56:05 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv5295 Modified Files: CommonSubs.pm Log Message: restore documentation for getNodeContentWithArticle moby-live/Perl/MOBY CommonSubs.pm,1.81,1.82 From kawas at dev.open-bio.org Thu Apr 27 11:10:49 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 27 Apr 2006 11:10:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271510.k3RFAn4O005394@dev.open-bio.org> kawas Thu Apr 27 11:10:49 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv5362/org/biomoby/client/ui/graphical/servlet/lsid/authority Modified Files: LSIDDataLookup.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority LSIDDataLookup.java,1.10,1.11 From mwilkinson at dev.open-bio.org Thu Apr 27 12:49:01 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 12:49:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271649.k3RGn1Z9005704@dev.open-bio.org> mwilkinson Thu Apr 27 12:49:01 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv5688/MOBY Modified Files: CommonSubs.pm Log Message: in fact, the paradigm is even easier if you set the output to be an empty string... no need for the final if block moby-live/Perl/MOBY CommonSubs.pm,1.82,1.83 From mwilkinson at dev.open-bio.org Thu Apr 27 12:50:28 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 12:50:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271650.k3RGoSon005741@dev.open-bio.org> mwilkinson Thu Apr 27 12:50:28 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv5725/Perl/scripts/Services Modified Files: LocalServices.pm Log Message: in fact, the paradigm is even easier if you set the output to be an empty string... no need for the final if block moby-live/Perl/scripts/Services LocalServices.pm,1.71,1.72 From mwilkinson at dev.open-bio.org Thu Apr 27 12:51:45 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 12:51:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271651.k3RGpjvB005778@dev.open-bio.org> mwilkinson Thu Apr 27 12:51:45 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv5762/Docs/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: in fact, the paradigm is even easier if you set the output to be an empty string... no need for the final if block moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.11,1.12 From mwilkinson at dev.open-bio.org Thu Apr 27 12:52:08 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 12:52:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271652.k3RGq8pX005815@dev.open-bio.org> mwilkinson Thu Apr 27 12:52:08 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv5799/Docs/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: in fact, the paradigm is even easier if you set the output to be an empty string... no need for the final if block moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.12,1.13 From mwilkinson at dev.open-bio.org Thu Apr 27 14:01:25 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 14:01:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271801.k3RI1PAN006009@dev.open-bio.org> mwilkinson Thu Apr 27 14:01:25 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv5993 Modified Files: CommonSubs.pm Log Message: oops. Forgot to export the new subroutine moby-live/Perl/MOBY CommonSubs.pm,1.83,1.84 From kawas at dev.open-bio.org Thu Apr 27 14:24:02 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 27 Apr 2006 14:24:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271824.k3RIO2jx006547@dev.open-bio.org> kawas Thu Apr 27 14:24:02 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv6514/org/biomoby/shared Modified Files: MobyObjectDecompositionImpl.java MobyObjectDecomposition.java Log Message: updated some predicates. Next update will use predicate library in org.biomoby.client.rdf.vocabulary instead of hard coding them. moby-live/Java/src/main/org/biomoby/shared MobyObjectDecompositionImpl.java,1.5,1.6 MobyObjectDecomposition.java,1.4,1.5 From mwilkinson at dev.open-bio.org Thu Apr 27 18:39:52 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 18:39:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604272239.k3RMdqRk011990@dev.open-bio.org> mwilkinson Thu Apr 27 18:39:52 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv11974 Modified Files: ConstructingYourService.html Log Message: new paradigm is even briefer if we set the default output to be empty string moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.13,1.14 From mwilkinson at dev.open-bio.org Thu Apr 27 18:42:23 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 18:42:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604272242.k3RMgNWf012028@dev.open-bio.org> mwilkinson Thu Apr 27 18:42:23 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv12012 Modified Files: RegisterServiceInstance.html Log Message: making docs fit space moby-live/Docs/MOBY-S_API/Perl RegisterServiceInstance.html,1.2,1.3 From senger at dev.open-bio.org Thu Apr 27 20:13:40 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0DePZ012186@dev.open-bio.org> senger Thu Apr 27 20:13:40 EDT 2006 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv12170 Modified Files: build.xml Log Message: moby-live/Java build.xml,1.53,1.54 From senger at dev.open-bio.org Thu Apr 27 20:13:40 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0Debg012205@dev.open-bio.org> senger Thu Apr 27 20:13:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv12170/docs Modified Files: ChangeLog Dashboard-NOTES.txt Download.html Log Message: moby-live/Java/docs ChangeLog,1.63,1.64 Dashboard-NOTES.txt,1.9,1.10 Download.html,1.6,1.7 From senger at dev.open-bio.org Thu Apr 27 20:13:40 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0De6V012220@dev.open-bio.org> senger Thu Apr 27 20:13:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv12170/src/Perl/MOBY/Datatypes Modified Files: MobyString.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyString.pm,1.3,1.4 From senger at dev.open-bio.org Thu Apr 27 20:13:40 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0DeLU012239@dev.open-bio.org> senger Thu Apr 27 20:13:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv12170/src/Perl/MOBY/Parser Modified Files: MobySimple.pm Log Message: moby-live/Java/src/Perl/MOBY/Parser MobySimple.pm,1.2,1.3 From senger at dev.open-bio.org Thu Apr 27 20:13:41 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0DfIC012352@dev.open-bio.org> senger Thu Apr 27 20:13:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv12170/xmls Added Files: dashboardBuild.xml deployBuild.xml mosesBuild.xml rdfagentBuild.xml samplesBuild.xml servletsBuild.xml Log Message: moby-live/Java/xmls dashboardBuild.xml,NONE,1.1 deployBuild.xml,NONE,1.1 mosesBuild.xml,NONE,1.1 rdfagentBuild.xml,NONE,1.1 samplesBuild.xml,NONE,1.1 servletsBuild.xml,NONE,1.1 From senger at dev.open-bio.org Thu Apr 27 20:13:41 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0Dfaf012334@dev.open-bio.org> senger Thu Apr 27 20:13:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv12170/src/main/org/biomoby/shared Modified Files: Utils.java Log Message: moby-live/Java/src/main/org/biomoby/shared Utils.java,1.12,1.13 From senger at dev.open-bio.org Thu Apr 27 20:13:41 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0DfUm012261@dev.open-bio.org> senger Thu Apr 27 20:13:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv12170/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java CentralDigestImpl.java Log Message: moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.17,1.18 CentralDigestImpl.java,1.10,1.11 From senger at dev.open-bio.org Thu Apr 27 20:13:41 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0DfMn012299@dev.open-bio.org> senger Thu Apr 27 20:13:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard In directory dev.open-bio.org:/tmp/cvs-serv12170/src/main/org/biomoby/service/dashboard Modified Files: CommonDataTable.java Dashboard.java DataTypesBoard.java DataTypesTree.java GeneratorPanel.java NamespacesBoard.java NamespacesTree.java RegistrationPanel.java RegistrationServiceSubPanel.java RegistryModel.java RegistryPanel.java SecondaryDataTable.java ServiceTypesBoard.java ServiceTypesTree.java ServicesBoard.java ServicesTree.java SimpleAnt.java SimpleClientPanel.java Log Message: moby-live/Java/src/main/org/biomoby/service/dashboard CommonDataTable.java,1.7,1.8 Dashboard.java,1.28,1.29 DataTypesBoard.java,1.13,1.14 DataTypesTree.java,1.15,1.16 GeneratorPanel.java,1.15,1.16 NamespacesBoard.java,1.8,1.9 NamespacesTree.java,1.9,1.10 RegistrationPanel.java,1.19,1.20 RegistrationServiceSubPanel.java,1.9,1.10 RegistryModel.java,1.19,1.20 RegistryPanel.java,1.26,1.27 SecondaryDataTable.java,1.4,1.5 ServiceTypesBoard.java,1.9,1.10 ServiceTypesTree.java,1.11,1.12 ServicesBoard.java,1.9,1.10 ServicesTree.java,1.13,1.14 SimpleAnt.java,1.4,1.5 SimpleClientPanel.java,1.7,1.8 From senger at dev.open-bio.org Thu Apr 27 20:13:41 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0DfR3012315@dev.open-bio.org> senger Thu Apr 27 20:13:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/data In directory dev.open-bio.org:/tmp/cvs-serv12170/src/main/org/biomoby/service/dashboard/data Modified Files: DataTypeTreeTable.java ParametersTable.java Log Message: moby-live/Java/src/main/org/biomoby/service/dashboard/data DataTypeTreeTable.java,1.11,1.12 ParametersTable.java,1.2,1.3 From senger at dev.open-bio.org Fri Apr 28 06:51:11 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 28 Apr 2006 06:51:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604281051.k3SApBYx013446@dev.open-bio.org> senger Fri Apr 28 06:51:11 EDT 2006 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv13430 Modified Files: build.xml Log Message: splitting jmoby.jar moby-live/Java build.xml,1.54,1.55 From mwilkinson at dev.open-bio.org Fri Apr 28 08:56:52 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Fri, 28 Apr 2006 08:56:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604281256.k3SCuqqI013647@dev.open-bio.org> mwilkinson Fri Apr 28 08:56:52 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13631/MOBY Modified Files: CommonSubs.pm Log Message: fixing docs in CommonSubs.pm moby-live/Perl/MOBY CommonSubs.pm,1.84,1.85 From mwilkinson at dev.open-bio.org Fri Apr 28 09:01:48 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Fri, 28 Apr 2006 09:01:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604281301.k3SD1mvl013686@dev.open-bio.org> mwilkinson Fri Apr 28 09:01:48 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13670/MOBY Modified Files: CommonSubs.pm Log Message: fixing docs in CommonSubs.pm moby-live/Perl/MOBY CommonSubs.pm,1.85,1.86 From mwilkinson at dev.open-bio.org Fri Apr 28 09:10:38 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Fri, 28 Apr 2006 09:10:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604281310.k3SDAcX4013750@dev.open-bio.org> mwilkinson Fri Apr 28 09:10:38 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13734/MOBY Modified Files: CommonSubs.pm Log Message: fixing docs in CommonSubs.pm moby-live/Perl/MOBY CommonSubs.pm,1.86,1.87 From senger at dev.open-bio.org Fri Apr 28 10:52:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 28 Apr 2006 10:52:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604281452.k3SEql3u014052@dev.open-bio.org> senger Fri Apr 28 10:52:47 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv14036/docs Modified Files: index.html Added Files: ServiceDevelopment.html empty_project.tar.gz Log Message: moby-live/Java/docs ServiceDevelopment.html,NONE,1.1 empty_project.tar.gz,NONE,1.1 index.html,1.22,1.23 From senger at dev.open-bio.org Fri Apr 28 10:52:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 28 Apr 2006 10:52:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604281452.k3SEqlhi014067@dev.open-bio.org> senger Fri Apr 28 10:52:47 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv14036/docs/images Modified Files: stylesheet.css Added Files: attention-smaller.gif Log Message: moby-live/Java/docs/images attention-smaller.gif,NONE,1.1 stylesheet.css,1.8,1.9 From gss at dev.open-bio.org Fri Apr 28 17:33:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 28 Apr 2006 17:33:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604282133.k3SLXEmc014762@dev.open-bio.org> gss Fri Apr 28 17:33:14 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/admin In directory dev.open-bio.org:/tmp/cvs-serv14728/admin Log Message: Directory /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/admin added to the repository s-moby/ref-impl/semanticmoby.org/WebRoot/admin - New directory From gss at dev.open-bio.org Fri Apr 28 17:33:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 28 Apr 2006 17:33:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604282133.k3SLXoUR014822@dev.open-bio.org> gss Fri Apr 28 17:33:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/admin In directory dev.open-bio.org:/tmp/cvs-serv14791/ref-impl/semanticmoby.org/WebRoot/admin Added Files: index.jsp Log Message: Placeholder s-moby/ref-impl/semanticmoby.org/WebRoot/admin index.jsp,NONE,1.1 From senger at dev.open-bio.org Sat Apr 29 17:22:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 29 Apr 2006 17:22:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604292122.k3TLMURB017078@dev.open-bio.org> senger Sat Apr 29 17:22:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv17062/docs Modified Files: Dashboard-NOTES.txt Log Message: add caller address to BaseService moby-live/Java/docs Dashboard-NOTES.txt,1.10,1.11 From senger at dev.open-bio.org Sat Apr 29 17:22:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 29 Apr 2006 17:22:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604292122.k3TLMUTr017095@dev.open-bio.org> senger Sat Apr 29 17:22:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service In directory dev.open-bio.org:/tmp/cvs-serv17062/src/main/org/biomoby/service Modified Files: BaseService.java Log Message: add caller address to BaseService moby-live/Java/src/main/org/biomoby/service BaseService.java,1.6,1.7 From senger at dev.open-bio.org Sat Apr 29 17:22:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 29 Apr 2006 17:22:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604292122.k3TLMUgP017129@dev.open-bio.org> senger Sat Apr 29 17:22:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv17062/xmls Modified Files: samplesBuild.xml Log Message: add caller address to BaseService moby-live/Java/xmls samplesBuild.xml,1.1,1.2 From senger at dev.open-bio.org Sat Apr 29 17:22:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 29 Apr 2006 17:22:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604292122.k3TLMUi3017110@dev.open-bio.org> senger Sat Apr 29 17:22:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service In directory dev.open-bio.org:/tmp/cvs-serv17062/src/samples/org/jmoby/tutorial/service Modified Files: HelloBiomobyWorldImpl.java Log Message: add caller address to BaseService moby-live/Java/src/samples/org/jmoby/tutorial/service HelloBiomobyWorldImpl.java,1.4,1.5 From llj at dev.open-bio.org Fri Apr 28 20:39:07 2006 From: llj at dev.open-bio.org (Linda Julien) Date: Sat, 29 Apr 2006 00:39:07 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200604290039.k3T0d4Zf015321@dev.open-bio.org> llj Fri Apr 28 20:39:03 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv15201 Modified Files: footer.jsp Added Files: login.jsp Log Message: Added login functionality for things in the /admin directory. NOTE: In order to use this, you'll need to add a 'smoby_admin' user to the tomcat-users.xml file in your tomcat/conf directory, and a role 'smoby_admin'. You can choose the password. There's now a logout link in the footer, as well. s-moby/ref-impl/semanticmoby.org/WebRoot login.jsp,NONE,1.1 footer.jsp,1.9,1.10 From llj at dev.open-bio.org Fri Apr 28 20:39:07 2006 From: llj at dev.open-bio.org (Linda Julien) Date: Sat, 29 Apr 2006 00:39:07 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200604290039.k3T0d4j7015336@dev.open-bio.org> llj Fri Apr 28 20:39:03 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv15201/WEB-INF Modified Files: web.xml Log Message: Added login functionality for things in the /admin directory. NOTE: In order to use this, you'll need to add a 'smoby_admin' user to the tomcat-users.xml file in your tomcat/conf directory, and a role 'smoby_admin'. You can choose the password. There's now a logout link in the footer, as well. s-moby/ref-impl/semanticmoby.org/WebRoot/WEB-INF web.xml,1.13,1.14 From llj at dev.open-bio.org Fri Apr 28 20:39:17 2006 From: llj at dev.open-bio.org (Linda Julien) Date: Sat, 29 Apr 2006 00:39:17 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200604290039.k3T0d48R015366@dev.open-bio.org> llj Fri Apr 28 20:39:03 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/css In directory dev.open-bio.org:/tmp/cvs-serv15201/css Modified Files: smoby.css Log Message: Added login functionality for things in the /admin directory. NOTE: In order to use this, you'll need to add a 'smoby_admin' user to the tomcat-users.xml file in your tomcat/conf directory, and a role 'smoby_admin'. You can choose the password. There's now a logout link in the footer, as well. s-moby/ref-impl/semanticmoby.org/WebRoot/css smoby.css,1.6,1.7 From llj at dev.open-bio.org Fri Apr 28 20:39:17 2006 From: llj at dev.open-bio.org (Linda Julien) Date: Sat, 29 Apr 2006 00:39:17 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200604290039.k3T0d4wa015351@dev.open-bio.org> llj Fri Apr 28 20:39:03 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/admin In directory dev.open-bio.org:/tmp/cvs-serv15201/admin Modified Files: index.jsp Log Message: Added login functionality for things in the /admin directory. NOTE: In order to use this, you'll need to add a 'smoby_admin' user to the tomcat-users.xml file in your tomcat/conf directory, and a role 'smoby_admin'. You can choose the password. There's now a logout link in the footer, as well. s-moby/ref-impl/semanticmoby.org/WebRoot/admin index.jsp,1.1,1.2 From llj at dev.open-bio.org Fri Apr 28 21:08:06 2006 From: llj at dev.open-bio.org (Linda Julien) Date: Sat, 29 Apr 2006 01:08:06 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200604290108.k3T185me015630@dev.open-bio.org> llj Fri Apr 28 21:08:05 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv15574 Modified Files: about.jsp contact.jsp footer.jsp header.jsp index.jsp Log Message: Brought these pages just a little bit closer to valid html. This includes: - don't end and in the header - don't start and in the footer - if a page includeds the header and footer, you don't need to start and end your own html (and, in fact, shouldn't) s-moby/ref-impl/semanticmoby.org/WebRoot about.jsp,1.6,1.7 contact.jsp,1.6,1.7 footer.jsp,1.10,1.11 header.jsp,1.14,1.15 index.jsp,1.10,1.11 From gss at dev.open-bio.org Mon Apr 3 23:28:37 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 3 Apr 2006 19:28:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604032328.k33NSbtR020406@dev.open-bio.org> gss Mon Apr 3 19:28:37 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools In directory dev.open-bio.org:/tmp/cvs-serv20374/src/org/semanticmoby/ref/tools Modified Files: MOBYProperties.java Log Message: Get location of properties file from smoby.properties-path system property s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools MOBYProperties.java,1.7,1.8 From gss at dev.open-bio.org Mon Apr 3 23:30:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 3 Apr 2006 19:30:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604032330.k33NUV9L020446@dev.open-bio.org> gss Mon Apr 3 19:30:31 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets In directory dev.open-bio.org:/tmp/cvs-serv20414/src/org/semanticmoby/ref/servlets Modified Files: InitServlet.java Log Message: Changes to work with changed MOBYProperties s-moby/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets InitServlet.java,1.2,1.3 From gss at dev.open-bio.org Mon Apr 3 23:33:29 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 3 Apr 2006 19:33:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604032333.k33NXTWr020486@dev.open-bio.org> gss Mon Apr 3 19:33:29 EDT 2006 Update of /home/repository/moby/s-moby In directory dev.open-bio.org:/tmp/cvs-serv20454 Modified Files: cvstag.log Log Message: Added entry for build-2006-4a s-moby cvstag.log,1.3,1.4 From mwilkinson at dev.open-bio.org Wed Apr 5 00:00:04 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 4 Apr 2006 20:00:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604050000.k350049f023999@dev.open-bio.org> mwilkinson Tue Apr 4 20:00:03 EDT 2006 Update of /home/repository/moby/moby-live/OWL In directory dev.open-bio.org:/tmp/cvs-serv23982 Modified Files: ServiceDescription.owl ServiceDescriptions.swp Log Message: OWL-DL ontology for MOBY services. Properly formatted Service Instance RDF should classify into this ontology as a serviceDescription object. moby-live/OWL ServiceDescription.owl,1.1,1.2 ServiceDescriptions.swp,1.1,1.2 From mwilkinson at dev.open-bio.org Wed Apr 5 00:05:46 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 4 Apr 2006 20:05:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604050005.k3505kaK024076@dev.open-bio.org> mwilkinson Tue Apr 4 20:05:46 EDT 2006 Update of /home/repository/moby/moby-live/OWL In directory dev.open-bio.org:/tmp/cvs-serv24060 Modified Files: ServiceDescription.owl Log Message: making the URI resolvable from the online CVS moby-live/OWL ServiceDescription.owl,1.2,1.3 From gss at dev.open-bio.org Wed Apr 5 20:43:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 5 Apr 2006 16:43:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604052043.k35KhI5K031629@dev.open-bio.org> gss Wed Apr 5 16:43:18 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java In directory dev.open-bio.org:/tmp/cvs-serv31595/src/java Log Message: Directory /home/repository/moby/s-moby/provider/src/java added to the repository s-moby/provider/src/java - New directory From gss at dev.open-bio.org Wed Apr 5 20:43:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 5 Apr 2006 16:43:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604052043.k35KhI5o031648@dev.open-bio.org> gss Wed Apr 5 16:43:18 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java/org In directory dev.open-bio.org:/tmp/cvs-serv31595/src/java/org Log Message: Directory /home/repository/moby/s-moby/provider/src/java/org added to the repository s-moby/provider/src/java/org - New directory From gss at dev.open-bio.org Wed Apr 5 20:43:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 5 Apr 2006 16:43:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604052043.k35KhI82031665@dev.open-bio.org> gss Wed Apr 5 16:43:18 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java/org/semanticmoby In directory dev.open-bio.org:/tmp/cvs-serv31595/src/java/org/semanticmoby Log Message: Directory /home/repository/moby/s-moby/provider/src/java/org/semanticmoby added to the repository s-moby/provider/src/java/org/semanticmoby - New directory From gss at dev.open-bio.org Wed Apr 5 20:43:18 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 5 Apr 2006 16:43:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604052043.k35KhI5D031688@dev.open-bio.org> gss Wed Apr 5 16:43:18 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java/org/semanticmoby/provider In directory dev.open-bio.org:/tmp/cvs-serv31595/src/java/org/semanticmoby/provider Log Message: Directory /home/repository/moby/s-moby/provider/src/java/org/semanticmoby/provider added to the repository s-moby/provider/src/java/org/semanticmoby/provider - New directory From gss at dev.open-bio.org Wed Apr 5 20:43:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 5 Apr 2006 16:43:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604052043.k35KhKrM031763@dev.open-bio.org> gss Wed Apr 5 16:43:20 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/org/semanticmoby/provider In directory dev.open-bio.org:/tmp/cvs-serv31715/src/org/semanticmoby/provider Removed Files: ParamReader.java AbstractMobyServlet.java ParameterException.java Log Message: Moved Java source files to from src/ to src/java s-moby/provider/src/org/semanticmoby/provider ParamReader.java,1.1,NONE AbstractMobyServlet.java,1.1,NONE ParameterException.java,1.1,NONE From gss at dev.open-bio.org Wed Apr 5 20:43:20 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 5 Apr 2006 16:43:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604052043.k35KhKaO031746@dev.open-bio.org> gss Wed Apr 5 16:43:20 EDT 2006 Update of /home/repository/moby/s-moby/provider/src/java/org/semanticmoby/provider In directory dev.open-bio.org:/tmp/cvs-serv31715/src/java/org/semanticmoby/provider Added Files: ParamReader.java AbstractMobyServlet.java ParameterException.java Log Message: Moved Java source files to from src/ to src/java s-moby/provider/src/java/org/semanticmoby/provider ParamReader.java,NONE,1.1 AbstractMobyServlet.java,NONE,1.1 ParameterException.java,NONE,1.1 From senger at dev.open-bio.org Wed Apr 5 15:55:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Wed, 5 Apr 2006 11:55:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604051555.k35FtlFR030412@dev.open-bio.org> senger Wed Apr 5 11:55:47 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv30396/src/Clients Removed Files: HelloMOBY2.java Log Message: moby-live/Java/src/Clients HelloMOBY2.java,1.1,NONE From ivanp at mmb.pcb.ub.es Wed Apr 5 14:18:24 2006 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Wed, 05 Apr 2006 16:18:24 +0200 Subject: [MOBY-guts] jMoby seems not to compile Message-ID: <4433D1B0.1000700@mmb.pcb.ub.es> Hi, Perhaps I'm committing some mistake but I think I've updated my local copy from the last version in the CVS and when I try to compile jMoby by doing "build-dev.sh all" I get the following error: compile-normal: [javac] Compiling 273 source files to /home/apache/moby-live/Java/build/classes [javac] Note: * uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] Compiling 20 source files to /home/apache/moby-live/Java/build/Clients [javac] /home/apache/moby-live/Java/src/Clients/HelloMOBY2.java:11: HelloMOBY2 is not abstract and does not override abstract method stop(org.biomoby.client.MobyRequest,int) in org.biomoby.client.MobyRequestEventHandler [javac] public class HelloMOBY2 implements MobyRequestEventHandler{ [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 1 error Best regards, -- Iv?n P?rraga Garc?a Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es http://mmb.pcb.ub.es From kawas at dev.open-bio.org Thu Apr 6 04:03:52 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 6 Apr 2006 00:03:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604060403.k3643qUZ032163@dev.open-bio.org> kawas Thu Apr 6 00:03:52 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv32130/org/biomoby/client/rdf/builder Modified Files: RDFConfigure.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder RDFConfigure.java,1.13,1.14 From gordonp at dev.open-bio.org Thu Apr 6 13:42:44 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 6 Apr 2006 09:42:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604061342.k36DgiRd000957@dev.open-bio.org> gordonp Thu Apr 6 09:42:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv924/src/Clients Added Files: HelloMOBY2.java Log Message: Updated to reflect change in MobyRequestEventHandler interface moby-live/Java/src/Clients HelloMOBY2.java,1.2,1.3 From kawas at dev.open-bio.org Thu Apr 6 22:07:38 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 6 Apr 2006 18:07:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604062207.k36M7cxu002253@dev.open-bio.org> kawas Thu Apr 6 18:07:38 EDT 2006 Update of /home/repository/moby/moby-live/OWL In directory dev.open-bio.org:/tmp/cvs-serv2222 Added Files: MOBYPredicates.owl Log Message: moby predicates moby-live/OWL MOBYPredicates.owl,NONE,1.1 From gss at dev.open-bio.org Fri Apr 7 16:42:27 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:42:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071642.k37GgRmi005939@dev.open-bio.org> gss Fri Apr 7 12:42:27 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web In directory dev.open-bio.org:/tmp/cvs-serv5908/examples/fasta-sequence/web Added Files: resourceProvider Log Message: Instance of moby:Provider to give information about the institution that provides resources s-moby/provider/examples/fasta-sequence/web resourceProvider,NONE,1.1 From gss at dev.open-bio.org Fri Apr 7 16:43:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:43:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071643.k37Ght5U005997@dev.open-bio.org> gss Fri Apr 7 12:43:55 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web In directory dev.open-bio.org:/tmp/cvs-serv5965/examples/fasta-sequence/web Modified Files: fasta-sequence.owl Log Message: Replaced providerName and providerAboutURI properties with providedBy property that refers to the resourceProvider individual s-moby/provider/examples/fasta-sequence/web fasta-sequence.owl,1.2,1.3 From gss at dev.open-bio.org Fri Apr 7 16:45:42 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:45:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071645.k37GjgpM006144@dev.open-bio.org> gss Fri Apr 7 12:45:42 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web/terms In directory dev.open-bio.org:/tmp/cvs-serv6113/examples/fasta-sequence/web/terms Added Files: owlOntology Log Message: owl:Ontology individual used to collectively document the terms in this ontology s-moby/provider/examples/fasta-sequence/web/terms owlOntology,NONE,1.1 From gss at dev.open-bio.org Fri Apr 7 16:45:57 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:45:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071645.k37Gjvew006185@dev.open-bio.org> gss Fri Apr 7 12:45:57 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web/terms In directory dev.open-bio.org:/tmp/cvs-serv6149/examples/fasta-sequence/web/terms Modified Files: tcNumber FastaKey FastaSequence speciesName sequenceText Log Message: Added reference to owlOntology individual s-moby/provider/examples/fasta-sequence/web/terms tcNumber,1.1,1.2 FastaKey,1.1,1.2 FastaSequence,1.1,1.2 speciesName,1.1,1.2 sequenceText,1.1,1.2 From gss at dev.open-bio.org Fri Apr 7 16:47:11 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:47:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071647.k37GlB3x006225@dev.open-bio.org> gss Fri Apr 7 12:47:11 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api/util In directory dev.open-bio.org:/tmp/cvs-serv6193/src/org/semanticmoby/api/util Modified Files: MOBY.java Log Message: Removed providerName and providerAboutURI properties; added providedBy and providesResource properties; added documentation on properties and classes s-moby/api/src/org/semanticmoby/api/util MOBY.java,1.1,1.2 From gss at dev.open-bio.org Fri Apr 7 16:51:24 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:51:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071651.k37GpOSJ006282@dev.open-bio.org> gss Fri Apr 7 12:51:24 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv6251/src/org/semanticmoby/api Added Files: MOBYProvider.java Log Message: Class to represent information about the provider of a set of MOBY resources s-moby/api/src/org/semanticmoby/api MOBYProvider.java,NONE,1.1 From gss at dev.open-bio.org Fri Apr 7 16:52:23 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:52:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071652.k37GqN0t006319@dev.open-bio.org> gss Fri Apr 7 12:52:23 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv6287/src/org/semanticmoby/api Modified Files: MOBYGraphNode.java Log Message: Added methods for setting and getting values of literal and resource properties s-moby/api/src/org/semanticmoby/api MOBYGraphNode.java,1.1,1.2 From gss at dev.open-bio.org Fri Apr 7 16:52:55 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:52:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071652.k37GqteW006356@dev.open-bio.org> gss Fri Apr 7 12:52:55 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv6324/src/org/semanticmoby/api Modified Files: MOBYResource.java Log Message: Removed providerName and providerAboutURI properties; added providedBy property s-moby/api/src/org/semanticmoby/api MOBYResource.java,1.1,1.2 From gss at dev.open-bio.org Fri Apr 7 16:54:08 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 12:54:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071654.k37Gs8Y8006396@dev.open-bio.org> gss Fri Apr 7 12:54:08 EDT 2006 Update of /home/repository/moby/s-moby/api/src/org/semanticmoby/api In directory dev.open-bio.org:/tmp/cvs-serv6364/src/org/semanticmoby/api Modified Files: Parser.java Log Message: Modified parseResource to no longer expect providerName and providerAboutURI properties, but to expect providedBy property; added parseProvider method s-moby/api/src/org/semanticmoby/api Parser.java,1.1,1.2 From lxm at dev.open-bio.org Fri Apr 7 16:59:21 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 7 Apr 2006 12:59:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071659.k37GxLlm006440@dev.open-bio.org> lxm Fri Apr 7 12:59:21 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv6406/web Log Message: Directory /home/repository/moby/s-moby/dclient/web added to the repository s-moby/dclient/web - New directory From lxm at dev.open-bio.org Fri Apr 7 17:00:17 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 7 Apr 2006 13:00:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071700.k37H0HfO006482@dev.open-bio.org> lxm Fri Apr 7 13:00:17 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv6448/WEB-INF Log Message: Directory /home/repository/moby/s-moby/dclient/web/WEB-INF added to the repository s-moby/dclient/web/WEB-INF - New directory From lxm at dev.open-bio.org Fri Apr 7 17:02:05 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Fri, 7 Apr 2006 13:02:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071702.k37H25fD006544@dev.open-bio.org> lxm Fri Apr 7 13:02:05 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv6513 Added Files: web.xml Log Message: web.xml file for discovery client web code s-moby/dclient/web/WEB-INF web.xml,NONE,1.1 From gss at dev.open-bio.org Fri Apr 7 17:47:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 7 Apr 2006 13:47:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604071747.k37Hle7D006776@dev.open-bio.org> gss Fri Apr 7 13:47:40 EDT 2006 Update of /home/repository/moby/s-moby/provider/examples/fasta-sequence/web/terms In directory dev.open-bio.org:/tmp/cvs-serv6744/provider/examples/fasta-sequence/web/terms Modified Files: owlOntology Log Message: Fixed a typo (missing quote) s-moby/provider/examples/fasta-sequence/web/terms owlOntology,1.1,1.2 From kawas at dev.open-bio.org Tue Apr 11 12:15:40 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 08:15:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111215.k3BCFevV032631@dev.open-bio.org> kawas Tue Apr 11 08:15:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv32599/MOBY/Parser Modified Files: MobyPackage.pm Log Message: moby-live/Java/src/Perl/MOBY/Parser MobyPackage.pm,1.2,1.3 From kawas at dev.open-bio.org Tue Apr 11 12:16:04 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 08:16:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111216.k3BCG4qC032704@dev.open-bio.org> kawas Tue Apr 11 08:16:04 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv32672/MOBY/Parser Modified Files: MobyParser.pm Log Message: moby-live/Java/src/Perl/MOBY/Parser MobyParser.pm,1.5,1.6 From kawas at dev.open-bio.org Tue Apr 11 12:16:54 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 08:16:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111216.k3BCGsjk032759@dev.open-bio.org> kawas Tue Apr 11 08:16:54 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv32727/MOBY/Parser Modified Files: MobyParameter.pm Log Message: moby-live/Java/src/Perl/MOBY/Parser MobyParameter.pm,1.2,1.3 From kawas at dev.open-bio.org Tue Apr 11 14:40:28 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 10:40:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111440.k3BEeSR2000529@dev.open-bio.org> kawas Tue Apr 11 10:40:28 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv498/org/biomoby/client/rdf/vocabulary Added Files: DC_PROTEGE.java Log Message: DC vocab that is owl-dl moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary DC_PROTEGE.java,NONE,1.1 From kawas at dev.open-bio.org Tue Apr 11 14:43:52 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 10:43:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111443.k3BEhqNr000569@dev.open-bio.org> kawas Tue Apr 11 10:43:52 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv537/org/biomoby/shared/extended Modified Files: ServiceTypeParser.java Log Message: updated to parse RDF that contains dc_protege. moby-live/Java/src/main/org/biomoby/shared/extended ServiceTypeParser.java,1.5,1.6 From kawas at dev.open-bio.org Tue Apr 11 14:45:00 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 10:45:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111445.k3BEj0ZG000609@dev.open-bio.org> kawas Tue Apr 11 10:45:00 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv577/org/biomoby/shared/extended Modified Files: NamespaceParser.java Log Message: updated to parse RDF that contains dc_protege. moby-live/Java/src/main/org/biomoby/shared/extended NamespaceParser.java,1.5,1.6 From kawas at dev.open-bio.org Tue Apr 11 14:46:15 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 10:46:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111446.k3BEkFP3000649@dev.open-bio.org> kawas Tue Apr 11 10:46:15 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv617/org/biomoby/shared/extended Modified Files: ServiceTypeParser.java Log Message: moby-live/Java/src/main/org/biomoby/shared/extended ServiceTypeParser.java,1.6,1.7 From kawas at dev.open-bio.org Tue Apr 11 14:48:40 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 10:48:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111448.k3BEmelY000707@dev.open-bio.org> kawas Tue Apr 11 10:48:39 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv675/org/biomoby/shared/extended Modified Files: DataTypeParser.java Log Message: updated to parse RDF that contains dc_protege. moby-live/Java/src/main/org/biomoby/shared/extended DataTypeParser.java,1.4,1.5 From kawas at dev.open-bio.org Tue Apr 11 14:57:52 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 10:57:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111457.k3BEvqSk000747@dev.open-bio.org> kawas Tue Apr 11 10:57:52 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv715/org/biomoby/shared/extended Modified Files: ServiceInstanceParser.java Log Message: updated to parse RDF that contains dc_protege. moby-live/Java/src/main/org/biomoby/shared/extended ServiceInstanceParser.java,1.13,1.14 From kawas at dev.open-bio.org Tue Apr 11 16:08:54 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 12:08:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111608.k3BG8ssW001304@dev.open-bio.org> kawas Tue Apr 11 12:08:54 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv1272/Perl/MOBY/Datatypes Modified Files: MobyInteger.pm Log Message: documented module moby-live/Java/src/Perl/MOBY/Datatypes MobyInteger.pm,1.1,1.2 From kawas at dev.open-bio.org Tue Apr 11 16:14:16 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 12:14:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111614.k3BGEGa3001344@dev.open-bio.org> kawas Tue Apr 11 12:14:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv1312/Perl/MOBY/Datatypes Modified Files: MobyFloat.pm Log Message: documented module moby-live/Java/src/Perl/MOBY/Datatypes MobyFloat.pm,1.1,1.2 From kawas at dev.open-bio.org Tue Apr 11 16:14:23 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 12:14:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111614.k3BGENlh001381@dev.open-bio.org> kawas Tue Apr 11 12:14:23 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv1349/Perl/MOBY/Datatypes Modified Files: MobyInteger.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyInteger.pm,1.2,1.3 From kawas at dev.open-bio.org Tue Apr 11 16:18:57 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 12:18:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111618.k3BGIvjA001423@dev.open-bio.org> kawas Tue Apr 11 12:18:57 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv1391/Perl/MOBY/Datatypes Modified Files: MobyFloat.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyFloat.pm,1.2,1.3 From kawas at dev.open-bio.org Tue Apr 11 17:02:09 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 13:02:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111702.k3BH29g9002041@dev.open-bio.org> kawas Tue Apr 11 13:02:09 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv2009/Perl/MOBY/Datatypes Modified Files: MobyObject.pm Log Message: documented module moby-live/Java/src/Perl/MOBY/Datatypes MobyObject.pm,1.4,1.5 From kawas at dev.open-bio.org Tue Apr 11 17:13:02 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 13:13:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111713.k3BHD2iL002119@dev.open-bio.org> kawas Tue Apr 11 13:13:02 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv2087/Perl/MOBY/Datatypes Modified Files: MobyString.pm Log Message: documented module moby-live/Java/src/Perl/MOBY/Datatypes MobyString.pm,1.1,1.2 From kawas at dev.open-bio.org Tue Apr 11 17:13:33 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 13:13:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604111713.k3BHDX9c002156@dev.open-bio.org> kawas Tue Apr 11 13:13:32 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv2124/Perl/MOBY/Datatypes Modified Files: MobyString.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyString.pm,1.2,1.3 From kawas at dev.open-bio.org Tue Apr 11 22:05:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 18:05:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604112205.k3BM5MjS002658@dev.open-bio.org> kawas Tue Apr 11 18:05:22 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv2625/Perl/MOBY/Parser Modified Files: MobyPackage.pm MobyJob.pm Log Message: fixed some array bugs. moby-live/Java/src/Perl/MOBY/Parser MobyPackage.pm,1.3,1.4 MobyJob.pm,1.2,1.3 From kawas at dev.open-bio.org Tue Apr 11 22:09:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 18:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604112209.k3BM9MOn002716@dev.open-bio.org> kawas Tue Apr 11 18:09:21 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv2684/Perl/MOBY/Parser Modified Files: MobyCollection.pm Log Message: modified the constructor () -> [] moby-live/Java/src/Perl/MOBY/Parser MobyCollection.pm,1.3,1.4 From kawas at dev.open-bio.org Tue Apr 11 22:46:33 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 11 Apr 2006 18:46:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604112246.k3BMkXMM002798@dev.open-bio.org> kawas Tue Apr 11 18:46:33 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv2766/Perl/MOBY/Parser Modified Files: MobyJob.pm Log Message: insertDataElement was adding properly to the array moby-live/Java/src/Perl/MOBY/Parser MobyJob.pm,1.3,1.4 From gss at dev.open-bio.org Mon Apr 17 18:38:35 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 17 Apr 2006 14:38:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604171838.k3HIcZIl003446@dev.open-bio.org> gss Mon Apr 17 14:38:35 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv3415 Added Files: SequenceOntology.tar.gz Log Message: Initial version on conversion from OBO format file to individual based ontology s-moby/ontologies SequenceOntology.tar.gz,NONE,1.1 From gss at dev.open-bio.org Mon Apr 17 18:39:13 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Mon, 17 Apr 2006 14:39:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604171839.k3HIdDY4003500@dev.open-bio.org> gss Mon Apr 17 14:39:13 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv3469/src/java/org/semanticmoby/ontologies/util Added Files: OBOConverter.java Log Message: General purpose converter for splitting an OBO format file into an individual based ontology s-moby/ontologies/src/java/org/semanticmoby/ontologies/util OBOConverter.java,NONE,1.1 From lxm at dev.open-bio.org Tue Apr 18 21:48:37 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 18 Apr 2006 17:48:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604182148.k3ILmb2l007480@dev.open-bio.org> lxm Tue Apr 18 17:48:37 EDT 2006 Update of /home/repository/moby/s-moby/dclient/src/org/semanticmoby/dclient In directory dev.open-bio.org:/tmp/cvs-serv7449 Added Files: AbstractDiscoveryClientServlet.java DataBean.java InvocationBroker.java KeywordSearchAllServlet.java KeywordSearchServlet.java ResourceEngagementServlet.java ResourceInvestigationServlet.java ResultsDisplayServlet.java Log Message: first round of separation of functionality, client servlets group s-moby/dclient/src/org/semanticmoby/dclient AbstractDiscoveryClientServlet.java,NONE,1.1 DataBean.java,NONE,1.1 InvocationBroker.java,NONE,1.1 KeywordSearchAllServlet.java,NONE,1.1 KeywordSearchServlet.java,NONE,1.1 ResourceEngagementServlet.java,NONE,1.1 ResourceInvestigationServlet.java,NONE,1.1 ResultsDisplayServlet.java,NONE,1.1 From lxm at dev.open-bio.org Tue Apr 18 21:51:04 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 18 Apr 2006 17:51:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604182151.k3ILp4lO007584@dev.open-bio.org> lxm Tue Apr 18 17:51:03 EDT 2006 Update of /home/repository/moby/s-moby/dserver/src/org/semanticmoby/dserver In directory dev.open-bio.org:/tmp/cvs-serv7551 Modified Files: MOBYProperties.java StorageManager.java Added Files: DiscoveryQuery.java DiscoveryServlet.java InitServlet.java InvestigationServlet.java KeywordDiscoveryServlet.java ParamReader.java ParameterException.java Log Message: second round of separation of functionality, server servlets s-moby/dserver/src/org/semanticmoby/dserver DiscoveryQuery.java,NONE,1.1 DiscoveryServlet.java,NONE,1.1 InitServlet.java,NONE,1.1 InvestigationServlet.java,NONE,1.1 KeywordDiscoveryServlet.java,NONE,1.1 ParamReader.java,NONE,1.1 ParameterException.java,NONE,1.1 MOBYProperties.java,1.1,1.2 StorageManager.java,1.1,1.2 From gss at dev.open-bio.org Tue Apr 18 23:33:40 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 18 Apr 2006 19:33:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604182333.k3INXelr007775@dev.open-bio.org> gss Tue Apr 18 19:33:40 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv7742/src/java/org/semanticmoby/ontologies/util Modified Files: OBOConverter.java Log Message: Create and reference an owl:Ontology individual; write Term individuals to termIndividuals subdirectory; copy input file to output directory s-moby/ontologies/src/java/org/semanticmoby/ontologies/util OBOConverter.java,1.1,1.2 From gss at dev.open-bio.org Tue Apr 18 23:36:33 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Tue, 18 Apr 2006 19:36:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604182336.k3INaXUD007835@dev.open-bio.org> gss Tue Apr 18 19:36:33 EDT 2006 Update of /home/repository/moby/s-moby/ontologies In directory dev.open-bio.org:/tmp/cvs-serv7803/ontologies Modified Files: SequenceOntology.tar.gz Log Message: Created and reference an owl:Ontology individual; Term individuals now in termIndividuals subdirectory; added so.obo input file to output directory s-moby/ontologies SequenceOntology.tar.gz,1.1,1.2 From kawas at dev.open-bio.org Wed Apr 19 18:46:07 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Apr 2006 14:46:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604191846.k3JIk7ke009893@dev.open-bio.org> kawas Wed Apr 19 14:46:06 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv9861/MOBY-S_API Modified Files: InputMessage.html Log Message: incorrect link for seconary inputs. moby-live/Docs/MOBY-S_API InputMessage.html,1.4,1.5 From kawas at dev.open-bio.org Wed Apr 19 21:34:46 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Apr 2006 17:34:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604192134.k3JLYk92010677@dev.open-bio.org> kawas Wed Apr 19 17:34:46 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/workflows In directory dev.open-bio.org:/tmp/cvs-serv10601/workflows Modified Files: 1 - workflow.xml 2 - blastDragonDbWorkflow.xml 4 - characterizeGeneticElement.xml 5 - BlastQueryAgainstAraProteinsE13.xml readme.txt 8 - hmm dragon workflow.xml 3 - cos_fixedInput.xml 6 - compareKeywordAndSimilarity.xml 1 - workflowInput.xml 7 - compareKeywordAndSimilarityAndPhytoprot_count.xml Added Files: 12 - TAIR_UBCFullWorkflow.xml 14 - BiomobyAndEMBOSSInteroperability.xml 13 - TAIR_UBCFullWorkflow-CollectionAsSimples.xml 16 - StringManipulationWorkflow.xml 15 - BiomobyAndEMBOSSInteroperability.xml 10 - GeneInfo workflow.xml 11 - KeggID2GeneInformation.xml Log Message: new workflows that work with the latest taverna plugin. most should be backwards compatible except for new ports that are used. moby-live/Java/docs/taverna/workflows 12 - TAIR_UBCFullWorkflow.xml,NONE,1.1 14 - BiomobyAndEMBOSSInteroperability.xml,NONE,1.1 13 - TAIR_UBCFullWorkflow-CollectionAsSimples.xml,NONE,1.1 16 - StringManipulationWorkflow.xml,NONE,1.1 15 - BiomobyAndEMBOSSInteroperability.xml,NONE,1.1 10 - GeneInfo workflow.xml,NONE,1.1 11 - KeggID2GeneInformation.xml,NONE,1.1 1 - workflow.xml,1.2,1.3 2 - blastDragonDbWorkflow.xml,1.2,1.3 4 - characterizeGeneticElement.xml,1.2,1.3 5 - BlastQueryAgainstAraProteinsE13.xml,1.2,1.3 readme.txt,1.1,1.2 8 - hmm dragon workflow.xml,1.1,1.2 3 - cos_fixedInput.xml,1.2,1.3 6 - compareKeywordAndSimilarity.xml,1.2,1.3 1 - workflowInput.xml,1.2,1.3 7 - compareKeywordAndSimilarityAndPhytoprot_count.xml,1.2,1.3 From kawas at dev.open-bio.org Wed Apr 19 21:52:02 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Apr 2006 17:52:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604192152.k3JLq2sB010856@dev.open-bio.org> kawas Wed Apr 19 17:52:02 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv10807/guide Modified Files: completeDnasequence.png serviceContextClick.png index.html workflowComplete.png objectTooltip.png results.png dnaConnectedMelting.png serviceTooltip.png addDNAtoModel.png tutorialWorkflowInput.xml contextObjectDetails.png workflows.html dnasequence.png objectContextMenu.png tutorialWorkflow.xml serviceDescription.png addingMelting.png msdAddToWorkflow.png Added Files: mobyservicediscovery.png email.png Log Message: updated guide for taverna 1.3.2-rc1 moby-live/Java/docs/taverna/guide mobyservicediscovery.png,NONE,1.1 email.png,NONE,1.1 completeDnasequence.png,1.1,1.2 serviceContextClick.png,1.1,1.2 index.html,1.4,1.5 workflowComplete.png,1.1,1.2 objectTooltip.png,1.1,1.2 results.png,1.1,1.2 dnaConnectedMelting.png,1.1,1.2 serviceTooltip.png,1.1,1.2 addDNAtoModel.png,1.1,1.2 tutorialWorkflowInput.xml,1.1,1.2 contextObjectDetails.png,1.1,1.2 workflows.html,1.3,1.4 dnasequence.png,1.1,1.2 objectContextMenu.png,1.1,1.2 tutorialWorkflow.xml,1.1,1.2 serviceDescription.png,1.1,1.2 addingMelting.png,1.1,1.2 msdAddToWorkflow.png,1.1,1.2 From gss at dev.open-bio.org Wed Apr 19 23:46:31 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 19 Apr 2006 19:46:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604192346.k3JNkVuZ011080@dev.open-bio.org> gss Wed Apr 19 19:46:31 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv11049/src/java/org/semanticmoby/ontologies/util Added Files: RDFFormatter.java Log Message: A class to help generate readable RDF/XML s-moby/ontologies/src/java/org/semanticmoby/ontologies/util RDFFormatter.java,NONE,1.1 From gss at dev.open-bio.org Wed Apr 19 23:46:58 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Wed, 19 Apr 2006 19:46:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604192346.k3JNkwle011117@dev.open-bio.org> gss Wed Apr 19 19:46:58 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv11085/src/java/org/semanticmoby/ontologies/util Modified Files: OBOConverter.java Log Message: Changed to use the RDFFormatter helper class s-moby/ontologies/src/java/org/semanticmoby/ontologies/util OBOConverter.java,1.2,1.3 From kawas at dev.open-bio.org Thu Apr 20 00:07:55 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Apr 2006 20:07:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604200007.k3K07t6s011180@dev.open-bio.org> kawas Wed Apr 19 20:07:55 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv11147/guide Modified Files: index.html Log Message: moby-live/Java/docs/taverna/guide index.html,1.5,1.6 From kawas at dev.open-bio.org Thu Apr 20 00:09:36 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 19 Apr 2006 20:09:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604200009.k3K09akg011220@dev.open-bio.org> kawas Wed Apr 19 20:09:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv11188/guide Modified Files: index.html Log Message: fixed another link moby-live/Java/docs/taverna/guide index.html,1.6,1.7 From kawas at dev.open-bio.org Thu Apr 20 15:05:16 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:05:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201505.k3KF5G7P013346@dev.open-bio.org> kawas Thu Apr 20 11:05:16 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv13314/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: dc -> dc_protege moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.16,1.17 From kawas at dev.open-bio.org Thu Apr 20 15:05:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:05:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201505.k3KF5hNX013400@dev.open-bio.org> kawas Thu Apr 20 11:05:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img In directory dev.open-bio.org:/tmp/cvs-serv13369/org/biomoby/client/ui/graphical/applets/img Added Files: blurredMoby.png Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/img blurredMoby.png,NONE,1.1 From kawas at dev.open-bio.org Thu Apr 20 15:07:22 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:07:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201507.k3KF7M9e013528@dev.open-bio.org> kawas Thu Apr 20 11:07:22 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared In directory dev.open-bio.org:/tmp/cvs-serv13497/org/biomoby/client/ui/graphical/applets/shared Added Files: ThreadWorker.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared ThreadWorker.java,NONE,1.1 From kawas at dev.open-bio.org Thu Apr 20 15:07:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:07:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201507.k3KF7hfn013631@dev.open-bio.org> kawas Thu Apr 20 11:07:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util In directory dev.open-bio.org:/tmp/cvs-serv13598/org/biomoby/client/ui/graphical/applets/util Modified Files: REGEXP.java Added Files: Authenticator.java LoadRDFTrees.java RDFProgressMonitor.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util Authenticator.java,NONE,1.1 LoadRDFTrees.java,NONE,1.1 RDFProgressMonitor.java,NONE,1.1 REGEXP.java,1.2,1.3 From kawas at dev.open-bio.org Thu Apr 20 15:07:56 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:07:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201507.k3KF7uVp013689@dev.open-bio.org> kawas Thu Apr 20 11:07:56 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool In directory dev.open-bio.org:/tmp/cvs-serv13656/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool Modified Files: NamespaceTree.java ServiceTypeTree.java Added Files: ServiceInstanceEditorWindow.java MobyDataTreeMouseListener.java SIMain.java PopUpWindow.java ServiceTypeMouseListener.java NamespaceKeyListener.java PrimaryInputOutputTableRender.java RegistrySelectWindow.java RegisterFormattedTextWindow.java NamespaceMouseListener.java ServiceTypeKeyListener.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool ServiceInstanceEditorWindow.java,NONE,1.1 MobyDataTreeMouseListener.java,NONE,1.1 SIMain.java,NONE,1.1 PopUpWindow.java,NONE,1.1 ServiceTypeMouseListener.java,NONE,1.1 NamespaceKeyListener.java,NONE,1.1 PrimaryInputOutputTableRender.java,NONE,1.1 RegistrySelectWindow.java,NONE,1.1 RegisterFormattedTextWindow.java,NONE,1.1 NamespaceMouseListener.java,NONE,1.1 ServiceTypeKeyListener.java,NONE,1.1 NamespaceTree.java,1.2,1.3 ServiceTypeTree.java,1.2,1.3 From kawas at dev.open-bio.org Thu Apr 20 15:08:18 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:08:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201508.k3KF8IkP013746@dev.open-bio.org> kawas Thu Apr 20 11:08:17 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms In directory dev.open-bio.org:/tmp/cvs-serv13715/org/biomoby/client/ui/graphical/servlet/forms Added Files: RDFAgentValidator.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/forms RDFAgentValidator.java,NONE,1.1 From kawas at dev.open-bio.org Thu Apr 20 15:08:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:08:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201508.k3KF8g5m013804@dev.open-bio.org> kawas Thu Apr 20 11:08:42 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources In directory dev.open-bio.org:/tmp/cvs-serv13772/org/biomoby/client/ui/graphical/servlet/jresources Modified Files: RESOURCE.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.15,1.16 From kawas at dev.open-bio.org Thu Apr 20 15:10:06 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:10:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201510.k3KFA6NQ013879@dev.open-bio.org> kawas Thu Apr 20 11:10:06 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central In directory dev.open-bio.org:/tmp/cvs-serv13848/org/biomoby/registry/Central Added Files: CentralImpl.java Log Message: moby-live/Java/src/main/org/biomoby/registry/Central CentralImpl.java,NONE,1.1 From kawas at dev.open-bio.org Thu Apr 20 15:10:14 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:10:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201510.k3KFAEmn013933@dev.open-bio.org> kawas Thu Apr 20 11:10:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central In directory dev.open-bio.org:/tmp/cvs-serv13902/org/biomoby/registry/Central Added Files: RegistryImpl.java Log Message: moby-live/Java/src/main/org/biomoby/registry/Central RegistryImpl.java,NONE,1.1 From kawas at dev.open-bio.org Thu Apr 20 15:10:44 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:10:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201510.k3KFAiHJ014010@dev.open-bio.org> kawas Thu Apr 20 11:10:44 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/properties In directory dev.open-bio.org:/tmp/cvs-serv13978/org/biomoby/registry/properties Modified Files: WindowsNT.java Log Message: moby-live/Java/src/main/org/biomoby/registry/properties WindowsNT.java,1.1,1.2 From kawas at dev.open-bio.org Thu Apr 20 15:15:49 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:15:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201515.k3KFFnLi014164@dev.open-bio.org> kawas Thu Apr 20 11:15:49 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central In directory dev.open-bio.org:/tmp/cvs-serv14131/org/biomoby/registry/Central Modified Files: CentralImpl.java Log Message: moby-live/Java/src/main/org/biomoby/registry/Central CentralImpl.java,1.1,1.2 From kawas at dev.open-bio.org Thu Apr 20 15:17:28 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:17:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201517.k3KFHSph014228@dev.open-bio.org> kawas Thu Apr 20 11:17:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central In directory dev.open-bio.org:/tmp/cvs-serv14196/org/biomoby/registry/Central Modified Files: RegistryImpl.java Log Message: moby-live/Java/src/main/org/biomoby/registry/Central RegistryImpl.java,1.1,1.2 From kawas at dev.open-bio.org Thu Apr 20 15:17:43 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 20 Apr 2006 11:17:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604201517.k3KFHhi9014265@dev.open-bio.org> kawas Thu Apr 20 11:17:43 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/registry/Central In directory dev.open-bio.org:/tmp/cvs-serv14233/org/biomoby/registry/Central Modified Files: RegistryImpl.java Log Message: moby-live/Java/src/main/org/biomoby/registry/Central RegistryImpl.java,1.2,1.3 From kawas at dev.open-bio.org Fri Apr 21 16:31:30 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Apr 2006 12:31:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604211631.k3LGVUfL022475@dev.open-bio.org> kawas Fri Apr 21 12:31:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv22442/Java/docs/taverna/guide Modified Files: workflows.html Log Message: fixed the layout so that it is more pleasing to the eye moby-live/Java/docs/taverna/guide workflows.html,1.4,1.5 From kawas at dev.open-bio.org Fri Apr 21 17:04:07 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 21 Apr 2006 13:04:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604211704.k3LH47U5022567@dev.open-bio.org> kawas Fri Apr 21 13:04:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory dev.open-bio.org:/tmp/cvs-serv22535/Java/docs/taverna/guide Modified Files: index.html Log Message: new question added some typos fixed moby-live/Java/docs/taverna/guide index.html,1.7,1.8 From gss at dev.open-bio.org Fri Apr 21 20:46:51 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 21 Apr 2006 16:46:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604212046.k3LKkpcr026624@dev.open-bio.org> gss Fri Apr 21 16:46:51 EDT 2006 Update of /home/repository/moby/s-moby/ontologies/src/java/org/semanticmoby/ontologies/util In directory dev.open-bio.org:/tmp/cvs-serv26591/src/java/org/semanticmoby/ontologies/util Modified Files: OBOConverter.java Log Message: Moved much of the functionality from main() into constructor and convert() method, in prepration for making a web deployment of this class s-moby/ontologies/src/java/org/semanticmoby/ontologies/util OBOConverter.java,1.3,1.4 From kawas at dev.open-bio.org Sun Apr 23 23:49:35 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Sun, 23 Apr 2006 19:49:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604232349.k3NNnZbG016820@dev.open-bio.org> kawas Sun Apr 23 19:49:35 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool In directory dev.open-bio.org:/tmp/cvs-serv16788/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool Modified Files: ServiceInstanceEditorWindow.java Log Message: commented out setMaximum/MinimumSize moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool ServiceInstanceEditorWindow.java,1.1,1.2 From kawas at dev.open-bio.org Mon Apr 24 13:11:14 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 24 Apr 2006 09:11:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604241311.k3ODBESf025815@dev.open-bio.org> kawas Mon Apr 24 09:11:14 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool In directory dev.open-bio.org:/tmp/cvs-serv25783/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool Modified Files: ServiceInstanceEditorWindow.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool ServiceInstanceEditorWindow.java,1.2,1.3 From kawas at dev.open-bio.org Mon Apr 24 14:20:30 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 24 Apr 2006 10:20:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604241420.k3OEKU43026021@dev.open-bio.org> kawas Mon Apr 24 10:20:29 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool In directory dev.open-bio.org:/tmp/cvs-serv25989 Modified Files: RegisterFormattedTextWindow.java Log Message: jvm 1.4 compat moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool RegisterFormattedTextWindow.java,1.1,1.2 From kawas at dev.open-bio.org Mon Apr 24 14:21:13 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 24 Apr 2006 10:21:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604241421.k3OELDSC026082@dev.open-bio.org> kawas Mon Apr 24 10:21:13 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util In directory dev.open-bio.org:/tmp/cvs-serv26050 Modified Files: RDFProgressMonitor.java Log Message: jvm 1.4 compat moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util RDFProgressMonitor.java,1.1,1.2 From mwilkinson at dev.open-bio.org Mon Apr 24 18:06:36 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Mon, 24 Apr 2006 14:06:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604241806.k3OI6aP1026540@dev.open-bio.org> mwilkinson Mon Apr 24 14:06:36 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv26524 Modified Files: ConstructingYourService.html Log Message: services require output article name - added this to the example moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.6,1.7 From lxm at dev.open-bio.org Tue Apr 25 17:48:38 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Apr 2006 13:48:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604251748.k3PHmcZK029021@dev.open-bio.org> lxm Tue Apr 25 13:48:38 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv28987/developer Log Message: Directory /home/repository/moby/s-moby/dclient/web/developer added to the repository s-moby/dclient/web/developer - New directory From lxm at dev.open-bio.org Tue Apr 25 17:50:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Apr 2006 13:50:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604251750.k3PHoMqP029102@dev.open-bio.org> lxm Tue Apr 25 13:50:22 EDT 2006 Update of /home/repository/moby/s-moby/dclient In directory dev.open-bio.org:/tmp/cvs-serv29071 Added Files: build.xml Log Message: jsp pages for the discovery client functionality s-moby/dclient build.xml,NONE,1.1 From lxm at dev.open-bio.org Tue Apr 25 17:50:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Apr 2006 13:50:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604251750.k3PHoMGc029116@dev.open-bio.org> lxm Tue Apr 25 13:50:22 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web In directory dev.open-bio.org:/tmp/cvs-serv29071/web Added Files: about.jsp contact.jsp data-header.jsp error.jsp footer.jsp header.jsp help.jsp index.jsp search-results.jsp sql-query.jsp Log Message: jsp pages for the discovery client functionality s-moby/dclient/web about.jsp,NONE,1.1 contact.jsp,NONE,1.1 data-header.jsp,NONE,1.1 error.jsp,NONE,1.1 footer.jsp,NONE,1.1 header.jsp,NONE,1.1 help.jsp,NONE,1.1 index.jsp,NONE,1.1 search-results.jsp,NONE,1.1 sql-query.jsp,NONE,1.1 From lxm at dev.open-bio.org Tue Apr 25 17:50:22 2006 From: lxm at dev.open-bio.org (Lonny Montoya) Date: Tue, 25 Apr 2006 13:50:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604251750.k3PHoMTA029134@dev.open-bio.org> lxm Tue Apr 25 13:50:22 EDT 2006 Update of /home/repository/moby/s-moby/dclient/web/developer In directory dev.open-bio.org:/tmp/cvs-serv29071/web/developer Added Files: acknowledge.jsp dev-tools.jsp index.jsp search.jsp suggest.jsp tech-overview.jsp Log Message: jsp pages for the discovery client functionality s-moby/dclient/web/developer acknowledge.jsp,NONE,1.1 dev-tools.jsp,NONE,1.1 index.jsp,NONE,1.1 search.jsp,NONE,1.1 suggest.jsp,NONE,1.1 tech-overview.jsp,NONE,1.1 From kawas at dev.open-bio.org Tue Apr 25 19:25:36 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 15:25:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604251925.k3PJPa3c029401@dev.open-bio.org> kawas Tue Apr 25 15:25:36 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool In directory dev.open-bio.org:/tmp/cvs-serv29369/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool Modified Files: SIMain.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool SIMain.java,1.1,1.2 From mwilkinson at dev.open-bio.org Tue Apr 25 21:13:41 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 25 Apr 2006 17:13:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252113.k3PLDfJ5029643@dev.open-bio.org> mwilkinson Tue Apr 25 17:13:41 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv29608/MOBY/Client Modified Files: CollectionArticle.pm SecondaryArticle.pm SimpleArticle.pm Log Message: fixing namespace problem with creating articles from XML DOM and updating documentation. moby-live/Perl/MOBY/Client CollectionArticle.pm,1.12,1.13 SecondaryArticle.pm,1.8,1.9 SimpleArticle.pm,1.9,1.10 From mwilkinson at dev.open-bio.org Tue Apr 25 21:13:41 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 25 Apr 2006 17:13:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252113.k3PLDfIt029624@dev.open-bio.org> mwilkinson Tue Apr 25 17:13:41 EDT 2006 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv29608 Modified Files: index.html Log Message: fixing namespace problem with creating articles from XML DOM and updating documentation. moby-live/Perl index.html,1.5,1.6 From mwilkinson at dev.open-bio.org Tue Apr 25 21:30:27 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 25 Apr 2006 17:30:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252130.k3PLURlF029810@dev.open-bio.org> mwilkinson Tue Apr 25 17:30:27 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv29792/MOBY/Client Modified Files: CollectionArticle.pm SecondaryArticle.pm SimpleArticle.pm Log Message: fixing namespace problem with creating articles from XML DOM and updating documentation. moby-live/Perl/MOBY/Client CollectionArticle.pm,1.13,1.14 SecondaryArticle.pm,1.9,1.10 SimpleArticle.pm,1.10,1.11 From mwilkinson at dev.open-bio.org Tue Apr 25 21:37:19 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 25 Apr 2006 17:37:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252137.k3PLbJXp029885@dev.open-bio.org> mwilkinson Tue Apr 25 17:37:19 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv29869/MOBY/Client Modified Files: SecondaryArticle.pm Log Message: fixing namespace problem with creating articles from XML DOM and updating documentation. moby-live/Perl/MOBY/Client SecondaryArticle.pm,1.10,1.11 From kawas at dev.open-bio.org Tue Apr 25 21:48:04 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 17:48:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252148.k3PLm4mk029943@dev.open-bio.org> kawas Tue Apr 25 17:48:04 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv29911/org/biomoby/client/rdf/builder Modified Files: RDFConfigure.java Log Message: convert to dc-protege moby-live/Java/src/main/org/biomoby/client/rdf/builder RDFConfigure.java,1.14,1.15 From kawas at dev.open-bio.org Tue Apr 25 21:48:47 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 17:48:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252148.k3PLmlUx029980@dev.open-bio.org> kawas Tue Apr 25 17:48:47 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv29948/org/biomoby/client/rdf/builder Modified Files: RDFConfigure.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder RDFConfigure.java,1.15,1.16 From mwilkinson at dev.open-bio.org Tue Apr 25 22:03:50 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 25 Apr 2006 18:03:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252203.k3PM3ogT030058@dev.open-bio.org> mwilkinson Tue Apr 25 18:03:50 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv30042/MOBY/Client Modified Files: SimpleArticle.pm Log Message: fixing namespace problem with creating articles from XML DOM and updating documentation. moby-live/Perl/MOBY/Client SimpleArticle.pm,1.11,1.12 From kawas at dev.open-bio.org Tue Apr 25 22:04:27 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 18:04:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252204.k3PM4R7v030116@dev.open-bio.org> kawas Tue Apr 25 18:04:27 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv30084/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.17,1.18 From kawas at dev.open-bio.org Tue Apr 25 22:30:12 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 18:30:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252230.k3PMUCNW030199@dev.open-bio.org> kawas Tue Apr 25 18:30:12 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv30167/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.18,1.19 From kawas at dev.open-bio.org Tue Apr 25 22:43:02 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 18:43:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252243.k3PMh27h030280@dev.open-bio.org> kawas Tue Apr 25 18:43:01 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv30248/org/biomoby/client/rdf/builder Modified Files: RDFConfigure.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder RDFConfigure.java,1.16,1.17 From kawas at dev.open-bio.org Tue Apr 25 23:49:07 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 19:49:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252349.k3PNn77b030368@dev.open-bio.org> kawas Tue Apr 25 19:49:07 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv30334/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java RDFConfigure.java Log Message: moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.19,1.20 RDFConfigure.java,1.17,1.18 From kawas at dev.open-bio.org Tue Apr 25 23:49:45 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 25 Apr 2006 19:49:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604252349.k3PNnjwp030441@dev.open-bio.org> kawas Tue Apr 25 19:49:45 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv30409/org/biomoby/client/ui/graphical/servlet/lsid/authority Modified Files: LSIDDataLookup.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority LSIDDataLookup.java,1.8,1.9 From senger at dev.open-bio.org Wed Apr 26 00:57:23 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Tue, 25 Apr 2006 20:57:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604260057.k3Q0vNda030706@dev.open-bio.org> senger Tue Apr 25 20:57:23 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv30688 Modified Files: ChangeLog Dashboard-NOTES.txt index.html Added Files: PMoses-NOTES.txt Log Message: moby-live/Java/docs PMoses-NOTES.txt,NONE,1.1 ChangeLog,1.62,1.63 Dashboard-NOTES.txt,1.8,1.9 index.html,1.21,1.22 From mwilkinson at dev.open-bio.org Wed Apr 26 12:16:18 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 08:16:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261216.k3QCGI0S032259@dev.open-bio.org> mwilkinson Wed Apr 26 08:16:18 EDT 2006 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv32243 Removed Files: index.html Log Message: index is now auto generated during the perl Makefile.PL moby-live/Perl index.html,1.6,NONE From mwilkinson at dev.open-bio.org Wed Apr 26 15:16:07 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 11:16:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261516.k3QFG7Lu000342@dev.open-bio.org> mwilkinson Wed Apr 26 11:16:07 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv326/MOBY Modified Files: CommonSubs.pm Log Message: TOTAL re-vamp of the CommonSubs code. New paradigm for building Perl services using a more OO approach. Still don't have objects to represent MOBY objects, but there are objects to represent Simple, Collection, and Secondary articles. Hello from the TIGR MOBY workshop\! moby-live/Perl/MOBY CommonSubs.pm,1.73,1.74 From mwilkinson at dev.open-bio.org Wed Apr 26 15:48:53 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 11:48:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261548.k3QFmr3P000647@dev.open-bio.org> mwilkinson Wed Apr 26 11:48:53 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv631/MOBY Modified Files: CommonSubs.pm Log Message: fixed typos in the example service moby-live/Perl/MOBY CommonSubs.pm,1.74,1.75 From mwilkinson at dev.open-bio.org Wed Apr 26 16:18:52 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 12:18:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261618.k3QGIq9s000805@dev.open-bio.org> mwilkinson Wed Apr 26 12:18:52 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv789/MOBY Modified Files: CommonSubs.pm Log Message: fixed typos in the example service moby-live/Perl/MOBY CommonSubs.pm,1.75,1.76 From mwilkinson at dev.open-bio.org Wed Apr 26 17:14:57 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 13:14:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261714.k3QHEvwq000999@dev.open-bio.org> mwilkinson Wed Apr 26 13:14:57 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv983/scripts/Services Modified Files: LocalServices.pm Log Message: fixed typos in the example service moby-live/Perl/scripts/Services LocalServices.pm,1.65,1.66 From mwilkinson at dev.open-bio.org Wed Apr 26 17:18:10 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 13:18:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261718.k3QHIAD0001038@dev.open-bio.org> mwilkinson Wed Apr 26 13:18:10 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv1022/scripts/Services Modified Files: LocalServices.pm Log Message: fixed typos in the example service moby-live/Perl/scripts/Services LocalServices.pm,1.66,1.67 From mwilkinson at dev.open-bio.org Wed Apr 26 17:20:57 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 13:20:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261720.k3QHKv9h001075@dev.open-bio.org> mwilkinson Wed Apr 26 13:20:57 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv1059/scripts/Services Modified Files: LocalServices.pm Log Message: fixed typos in the example service moby-live/Perl/scripts/Services LocalServices.pm,1.67,1.68 From mwilkinson at dev.open-bio.org Wed Apr 26 17:47:33 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 13:47:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261747.k3QHlXW5001192@dev.open-bio.org> mwilkinson Wed Apr 26 13:47:33 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv1176/Docs/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: updating the docs for creating your service moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.7,1.8 From mwilkinson at dev.open-bio.org Wed Apr 26 18:11:11 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 14:11:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261811.k3QIBBRG001270@dev.open-bio.org> mwilkinson Wed Apr 26 14:11:11 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv1253/MOBY/Client Modified Files: CollectionArticle.pm SimpleArticle.pm Log Message: complete the object by extracting the raw XML from the DOM so that it is easily accessible as per the objects API moby-live/Perl/MOBY/Client CollectionArticle.pm,1.14,1.15 SimpleArticle.pm,1.12,1.13 From mwilkinson at dev.open-bio.org Wed Apr 26 19:58:44 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 15:58:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604261958.k3QJwiJ4001483@dev.open-bio.org> mwilkinson Wed Apr 26 15:58:44 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv1467/MOBY Modified Files: CommonSubs.pm Log Message: fixing docs in CommonSubs moby-live/Perl/MOBY CommonSubs.pm,1.76,1.77 From mwilkinson at dev.open-bio.org Wed Apr 26 20:17:55 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Wed, 26 Apr 2006 16:17:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604262017.k3QKHtH3001565@dev.open-bio.org> mwilkinson Wed Apr 26 16:17:55 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv1549/MOBY Modified Files: CommonSubs.pm Log Message: fixing docs in CommonSubs moby-live/Perl/MOBY CommonSubs.pm,1.77,1.78 From mwilkinson at dev.open-bio.org Thu Apr 27 10:39:23 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 06:39:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271039.k3RAdNnw003868@dev.open-bio.org> mwilkinson Thu Apr 27 06:39:22 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv3852/Perl/MOBY Modified Files: CommonSubs.pm Log Message: changed the CommonSubs input parser one more time to make it a hash of hashes. Inputs are accessible by their articleName. We are DEFINITELY no longer backwards compatible with the old API. moby-live/Perl/MOBY CommonSubs.pm,1.78,1.79 From mwilkinson at dev.open-bio.org Thu Apr 27 10:40:06 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 06:40:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271040.k3RAe6jV003905@dev.open-bio.org> mwilkinson Thu Apr 27 06:40:06 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv3889/Docs/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: updating the docs for the new CommonSubs moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.8,1.9 From mwilkinson at dev.open-bio.org Thu Apr 27 10:52:43 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 06:52:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271052.k3RAqhY6003978@dev.open-bio.org> mwilkinson Thu Apr 27 06:52:43 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv3962/Docs/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: updating docs with a better paradigm moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.9,1.10 From mwilkinson at dev.open-bio.org Thu Apr 27 10:55:03 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 06:55:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271055.k3RAt3dH004015@dev.open-bio.org> mwilkinson Thu Apr 27 06:55:03 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv3999/Perl/MOBY Modified Files: CommonSubs.pm Log Message: updating docs with a better paradigm moby-live/Perl/MOBY CommonSubs.pm,1.79,1.80 From mwilkinson at dev.open-bio.org Thu Apr 27 13:34:02 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 09:34:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271334.k3RDY2cK004200@dev.open-bio.org> mwilkinson Thu Apr 27 09:34:02 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv4184 Modified Files: LocalServices.pm Log Message: updated sample LocalServices file with the new service code paradigm moby-live/Perl/scripts/Services LocalServices.pm,1.68,1.69 From mwilkinson at dev.open-bio.org Thu Apr 27 13:34:46 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 09:34:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271334.k3RDYksG004237@dev.open-bio.org> mwilkinson Thu Apr 27 09:34:46 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts In directory dev.open-bio.org:/tmp/cvs-serv4221 Modified Files: Services.cgi Log Message: sample dispatcher now has only one service in LocalServices.pm moby-live/Perl/scripts Services.cgi,1.5,1.6 From mwilkinson at dev.open-bio.org Thu Apr 27 14:14:25 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 10:14:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271414.k3REEPIW004596@dev.open-bio.org> mwilkinson Thu Apr 27 10:14:25 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv4580/Services Modified Files: LocalServices.pm Log Message: added a scaffold example of a service that returns collections moby-live/Perl/scripts/Services LocalServices.pm,1.69,1.70 From mwilkinson at dev.open-bio.org Thu Apr 27 14:29:43 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 10:29:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271429.k3REThAP004635@dev.open-bio.org> mwilkinson Thu Apr 27 10:29:43 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv4619 Modified Files: LocalServices.pm Log Message: added a scaffold example of a service that returns collections moby-live/Perl/scripts/Services LocalServices.pm,1.70,1.71 From mwilkinson at dev.open-bio.org Thu Apr 27 14:31:32 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 10:31:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271431.k3REVWvV004714@dev.open-bio.org> mwilkinson Thu Apr 27 10:31:32 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv4698 Modified Files: CommonSubs.pm Log Message: added an example of a service that returns collections moby-live/Perl/MOBY CommonSubs.pm,1.80,1.81 From mwilkinson at dev.open-bio.org Thu Apr 27 14:33:29 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 10:33:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271433.k3REXTAi004793@dev.open-bio.org> mwilkinson Thu Apr 27 10:33:29 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv4777 Modified Files: ConstructingYourService.html Log Message: added a collection service example moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.10,1.11 From kawas at dev.open-bio.org Thu Apr 27 14:47:37 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 27 Apr 2006 10:47:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271447.k3RElb4A005157@dev.open-bio.org> kawas Thu Apr 27 10:47:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv5122/org/biomoby/shared/extended Modified Files: NamespaceParser.java DataTypeParser.java ServiceInstanceParser.java ServiceTypeParser.java Log Message: updated the RDF and its generators so that nodes in the rdf use URIs and LSIDs are not contained as a property, dublincore identifier. Parsers have been modified so that they can handle this RDF. moby-live/Java/src/main/org/biomoby/shared/extended NamespaceParser.java,1.6,1.7 DataTypeParser.java,1.5,1.6 ServiceInstanceParser.java,1.14,1.15 ServiceTypeParser.java,1.7,1.8 From kawas at dev.open-bio.org Thu Apr 27 14:47:37 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 27 Apr 2006 10:47:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271447.k3RElbXa005173@dev.open-bio.org> kawas Thu Apr 27 10:47:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory dev.open-bio.org:/tmp/cvs-serv5122/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java RDFConfigure.java Log Message: updated the RDF and its generators so that nodes in the rdf use URIs and LSIDs are not contained as a property, dublincore identifier. Parsers have been modified so that they can handle this RDF. moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.20,1.21 RDFConfigure.java,1.18,1.19 From kawas at dev.open-bio.org Thu Apr 27 14:47:37 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 27 Apr 2006 10:47:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271447.k3RElbiC005214@dev.open-bio.org> kawas Thu Apr 27 10:47:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources In directory dev.open-bio.org:/tmp/cvs-serv5122/org/biomoby/client/ui/graphical/servlet/jresources Modified Files: RESOURCE.java Log Message: updated the RDF and its generators so that nodes in the rdf use URIs and LSIDs are not contained as a property, dublincore identifier. Parsers have been modified so that they can handle this RDF. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.16,1.17 From kawas at dev.open-bio.org Thu Apr 27 14:47:37 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 27 Apr 2006 10:47:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271447.k3RElbXQ005229@dev.open-bio.org> kawas Thu Apr 27 10:47:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv5122/org/biomoby/client/rdf/vocabulary Modified Files: DC_PROTEGE.java Log Message: updated the RDF and its generators so that nodes in the rdf use URIs and LSIDs are not contained as a property, dublincore identifier. Parsers have been modified so that they can handle this RDF. moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary DC_PROTEGE.java,1.1,1.2 From kawas at dev.open-bio.org Thu Apr 27 14:47:37 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 27 Apr 2006 10:47:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271447.k3RElben005193@dev.open-bio.org> kawas Thu Apr 27 10:47:37 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv5122/org/biomoby/client/ui/graphical/servlet/lsid/authority Modified Files: LSIDAuthorityMetaData.java LSIDDataLookup.java Log Message: updated the RDF and its generators so that nodes in the rdf use URIs and LSIDs are not contained as a property, dublincore identifier. Parsers have been modified so that they can handle this RDF. moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority LSIDAuthorityMetaData.java,1.6,1.7 LSIDDataLookup.java,1.9,1.10 From mwilkinson at dev.open-bio.org Thu Apr 27 14:56:05 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 10:56:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271456.k3REu5SA005311@dev.open-bio.org> mwilkinson Thu Apr 27 10:56:05 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv5295 Modified Files: CommonSubs.pm Log Message: restore documentation for getNodeContentWithArticle moby-live/Perl/MOBY CommonSubs.pm,1.81,1.82 From kawas at dev.open-bio.org Thu Apr 27 15:10:49 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 27 Apr 2006 11:10:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271510.k3RFAn4O005394@dev.open-bio.org> kawas Thu Apr 27 11:10:49 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv5362/org/biomoby/client/ui/graphical/servlet/lsid/authority Modified Files: LSIDDataLookup.java Log Message: moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/lsid/authority LSIDDataLookup.java,1.10,1.11 From mwilkinson at dev.open-bio.org Thu Apr 27 16:49:01 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 12:49:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271649.k3RGn1Z9005704@dev.open-bio.org> mwilkinson Thu Apr 27 12:49:01 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv5688/MOBY Modified Files: CommonSubs.pm Log Message: in fact, the paradigm is even easier if you set the output to be an empty string... no need for the final if block moby-live/Perl/MOBY CommonSubs.pm,1.82,1.83 From mwilkinson at dev.open-bio.org Thu Apr 27 16:50:28 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 12:50:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271650.k3RGoSon005741@dev.open-bio.org> mwilkinson Thu Apr 27 12:50:28 EDT 2006 Update of /home/repository/moby/moby-live/Perl/scripts/Services In directory dev.open-bio.org:/tmp/cvs-serv5725/Perl/scripts/Services Modified Files: LocalServices.pm Log Message: in fact, the paradigm is even easier if you set the output to be an empty string... no need for the final if block moby-live/Perl/scripts/Services LocalServices.pm,1.71,1.72 From mwilkinson at dev.open-bio.org Thu Apr 27 16:51:45 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 12:51:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271651.k3RGpjvB005778@dev.open-bio.org> mwilkinson Thu Apr 27 12:51:45 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv5762/Docs/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: in fact, the paradigm is even easier if you set the output to be an empty string... no need for the final if block moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.11,1.12 From mwilkinson at dev.open-bio.org Thu Apr 27 16:52:08 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 12:52:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271652.k3RGq8pX005815@dev.open-bio.org> mwilkinson Thu Apr 27 12:52:08 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv5799/Docs/MOBY-S_API/Perl Modified Files: ConstructingYourService.html Log Message: in fact, the paradigm is even easier if you set the output to be an empty string... no need for the final if block moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.12,1.13 From mwilkinson at dev.open-bio.org Thu Apr 27 18:01:25 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 14:01:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271801.k3RI1PAN006009@dev.open-bio.org> mwilkinson Thu Apr 27 14:01:25 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv5993 Modified Files: CommonSubs.pm Log Message: oops. Forgot to export the new subroutine moby-live/Perl/MOBY CommonSubs.pm,1.83,1.84 From kawas at dev.open-bio.org Thu Apr 27 18:24:02 2006 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Thu, 27 Apr 2006 14:24:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604271824.k3RIO2jx006547@dev.open-bio.org> kawas Thu Apr 27 14:24:02 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv6514/org/biomoby/shared Modified Files: MobyObjectDecompositionImpl.java MobyObjectDecomposition.java Log Message: updated some predicates. Next update will use predicate library in org.biomoby.client.rdf.vocabulary instead of hard coding them. moby-live/Java/src/main/org/biomoby/shared MobyObjectDecompositionImpl.java,1.5,1.6 MobyObjectDecomposition.java,1.4,1.5 From mwilkinson at dev.open-bio.org Thu Apr 27 22:39:52 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 18:39:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604272239.k3RMdqRk011990@dev.open-bio.org> mwilkinson Thu Apr 27 18:39:52 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv11974 Modified Files: ConstructingYourService.html Log Message: new paradigm is even briefer if we set the default output to be empty string moby-live/Docs/MOBY-S_API/Perl ConstructingYourService.html,1.13,1.14 From mwilkinson at dev.open-bio.org Thu Apr 27 22:42:23 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Thu, 27 Apr 2006 18:42:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604272242.k3RMgNWf012028@dev.open-bio.org> mwilkinson Thu Apr 27 18:42:23 EDT 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv12012 Modified Files: RegisterServiceInstance.html Log Message: making docs fit space moby-live/Docs/MOBY-S_API/Perl RegisterServiceInstance.html,1.2,1.3 From senger at dev.open-bio.org Fri Apr 28 00:13:40 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0DePZ012186@dev.open-bio.org> senger Thu Apr 27 20:13:40 EDT 2006 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv12170 Modified Files: build.xml Log Message: moby-live/Java build.xml,1.53,1.54 From senger at dev.open-bio.org Fri Apr 28 00:13:40 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0Debg012205@dev.open-bio.org> senger Thu Apr 27 20:13:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv12170/docs Modified Files: ChangeLog Dashboard-NOTES.txt Download.html Log Message: moby-live/Java/docs ChangeLog,1.63,1.64 Dashboard-NOTES.txt,1.9,1.10 Download.html,1.6,1.7 From senger at dev.open-bio.org Fri Apr 28 00:13:40 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0De6V012220@dev.open-bio.org> senger Thu Apr 27 20:13:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Datatypes In directory dev.open-bio.org:/tmp/cvs-serv12170/src/Perl/MOBY/Datatypes Modified Files: MobyString.pm Log Message: moby-live/Java/src/Perl/MOBY/Datatypes MobyString.pm,1.3,1.4 From senger at dev.open-bio.org Fri Apr 28 00:13:40 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0DeLU012239@dev.open-bio.org> senger Thu Apr 27 20:13:40 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/Perl/MOBY/Parser In directory dev.open-bio.org:/tmp/cvs-serv12170/src/Perl/MOBY/Parser Modified Files: MobySimple.pm Log Message: moby-live/Java/src/Perl/MOBY/Parser MobySimple.pm,1.2,1.3 From senger at dev.open-bio.org Fri Apr 28 00:13:41 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0DfIC012352@dev.open-bio.org> senger Thu Apr 27 20:13:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv12170/xmls Added Files: dashboardBuild.xml deployBuild.xml mosesBuild.xml rdfagentBuild.xml samplesBuild.xml servletsBuild.xml Log Message: moby-live/Java/xmls dashboardBuild.xml,NONE,1.1 deployBuild.xml,NONE,1.1 mosesBuild.xml,NONE,1.1 rdfagentBuild.xml,NONE,1.1 samplesBuild.xml,NONE,1.1 servletsBuild.xml,NONE,1.1 From senger at dev.open-bio.org Fri Apr 28 00:13:41 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0Dfaf012334@dev.open-bio.org> senger Thu Apr 27 20:13:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv12170/src/main/org/biomoby/shared Modified Files: Utils.java Log Message: moby-live/Java/src/main/org/biomoby/shared Utils.java,1.12,1.13 From senger at dev.open-bio.org Fri Apr 28 00:13:41 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0DfUm012261@dev.open-bio.org> senger Thu Apr 27 20:13:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv12170/src/main/org/biomoby/client Modified Files: CentralDigestCachedImpl.java CentralDigestImpl.java Log Message: moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.17,1.18 CentralDigestImpl.java,1.10,1.11 From senger at dev.open-bio.org Fri Apr 28 00:13:41 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0DfMn012299@dev.open-bio.org> senger Thu Apr 27 20:13:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard In directory dev.open-bio.org:/tmp/cvs-serv12170/src/main/org/biomoby/service/dashboard Modified Files: CommonDataTable.java Dashboard.java DataTypesBoard.java DataTypesTree.java GeneratorPanel.java NamespacesBoard.java NamespacesTree.java RegistrationPanel.java RegistrationServiceSubPanel.java RegistryModel.java RegistryPanel.java SecondaryDataTable.java ServiceTypesBoard.java ServiceTypesTree.java ServicesBoard.java ServicesTree.java SimpleAnt.java SimpleClientPanel.java Log Message: moby-live/Java/src/main/org/biomoby/service/dashboard CommonDataTable.java,1.7,1.8 Dashboard.java,1.28,1.29 DataTypesBoard.java,1.13,1.14 DataTypesTree.java,1.15,1.16 GeneratorPanel.java,1.15,1.16 NamespacesBoard.java,1.8,1.9 NamespacesTree.java,1.9,1.10 RegistrationPanel.java,1.19,1.20 RegistrationServiceSubPanel.java,1.9,1.10 RegistryModel.java,1.19,1.20 RegistryPanel.java,1.26,1.27 SecondaryDataTable.java,1.4,1.5 ServiceTypesBoard.java,1.9,1.10 ServiceTypesTree.java,1.11,1.12 ServicesBoard.java,1.9,1.10 ServicesTree.java,1.13,1.14 SimpleAnt.java,1.4,1.5 SimpleClientPanel.java,1.7,1.8 From senger at dev.open-bio.org Fri Apr 28 00:13:41 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 27 Apr 2006 20:13:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604280013.k3S0DfR3012315@dev.open-bio.org> senger Thu Apr 27 20:13:41 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/data In directory dev.open-bio.org:/tmp/cvs-serv12170/src/main/org/biomoby/service/dashboard/data Modified Files: DataTypeTreeTable.java ParametersTable.java Log Message: moby-live/Java/src/main/org/biomoby/service/dashboard/data DataTypeTreeTable.java,1.11,1.12 ParametersTable.java,1.2,1.3 From senger at dev.open-bio.org Fri Apr 28 10:51:11 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 28 Apr 2006 06:51:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604281051.k3SApBYx013446@dev.open-bio.org> senger Fri Apr 28 06:51:11 EDT 2006 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv13430 Modified Files: build.xml Log Message: splitting jmoby.jar moby-live/Java build.xml,1.54,1.55 From mwilkinson at dev.open-bio.org Fri Apr 28 12:56:52 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Fri, 28 Apr 2006 08:56:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604281256.k3SCuqqI013647@dev.open-bio.org> mwilkinson Fri Apr 28 08:56:52 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13631/MOBY Modified Files: CommonSubs.pm Log Message: fixing docs in CommonSubs.pm moby-live/Perl/MOBY CommonSubs.pm,1.84,1.85 From mwilkinson at dev.open-bio.org Fri Apr 28 13:01:48 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Fri, 28 Apr 2006 09:01:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604281301.k3SD1mvl013686@dev.open-bio.org> mwilkinson Fri Apr 28 09:01:48 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13670/MOBY Modified Files: CommonSubs.pm Log Message: fixing docs in CommonSubs.pm moby-live/Perl/MOBY CommonSubs.pm,1.85,1.86 From mwilkinson at dev.open-bio.org Fri Apr 28 13:10:38 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Fri, 28 Apr 2006 09:10:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604281310.k3SDAcX4013750@dev.open-bio.org> mwilkinson Fri Apr 28 09:10:38 EDT 2006 Update of /home/repository/moby/moby-live/Perl/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13734/MOBY Modified Files: CommonSubs.pm Log Message: fixing docs in CommonSubs.pm moby-live/Perl/MOBY CommonSubs.pm,1.86,1.87 From senger at dev.open-bio.org Fri Apr 28 14:52:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 28 Apr 2006 10:52:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604281452.k3SEql3u014052@dev.open-bio.org> senger Fri Apr 28 10:52:47 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv14036/docs Modified Files: index.html Added Files: ServiceDevelopment.html empty_project.tar.gz Log Message: moby-live/Java/docs ServiceDevelopment.html,NONE,1.1 empty_project.tar.gz,NONE,1.1 index.html,1.22,1.23 From senger at dev.open-bio.org Fri Apr 28 14:52:47 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Fri, 28 Apr 2006 10:52:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604281452.k3SEqlhi014067@dev.open-bio.org> senger Fri Apr 28 10:52:47 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs/images In directory dev.open-bio.org:/tmp/cvs-serv14036/docs/images Modified Files: stylesheet.css Added Files: attention-smaller.gif Log Message: moby-live/Java/docs/images attention-smaller.gif,NONE,1.1 stylesheet.css,1.8,1.9 From gss at dev.open-bio.org Fri Apr 28 21:33:14 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 28 Apr 2006 17:33:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604282133.k3SLXEmc014762@dev.open-bio.org> gss Fri Apr 28 17:33:14 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/admin In directory dev.open-bio.org:/tmp/cvs-serv14728/admin Log Message: Directory /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/admin added to the repository s-moby/ref-impl/semanticmoby.org/WebRoot/admin - New directory From gss at dev.open-bio.org Fri Apr 28 21:33:50 2006 From: gss at dev.open-bio.org (Gary Schiltz) Date: Fri, 28 Apr 2006 17:33:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604282133.k3SLXoUR014822@dev.open-bio.org> gss Fri Apr 28 17:33:50 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/admin In directory dev.open-bio.org:/tmp/cvs-serv14791/ref-impl/semanticmoby.org/WebRoot/admin Added Files: index.jsp Log Message: Placeholder s-moby/ref-impl/semanticmoby.org/WebRoot/admin index.jsp,NONE,1.1 From senger at dev.open-bio.org Sat Apr 29 21:22:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 29 Apr 2006 17:22:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604292122.k3TLMURB017078@dev.open-bio.org> senger Sat Apr 29 17:22:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv17062/docs Modified Files: Dashboard-NOTES.txt Log Message: add caller address to BaseService moby-live/Java/docs Dashboard-NOTES.txt,1.10,1.11 From senger at dev.open-bio.org Sat Apr 29 21:22:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 29 Apr 2006 17:22:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604292122.k3TLMUTr017095@dev.open-bio.org> senger Sat Apr 29 17:22:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service In directory dev.open-bio.org:/tmp/cvs-serv17062/src/main/org/biomoby/service Modified Files: BaseService.java Log Message: add caller address to BaseService moby-live/Java/src/main/org/biomoby/service BaseService.java,1.6,1.7 From senger at dev.open-bio.org Sat Apr 29 21:22:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 29 Apr 2006 17:22:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604292122.k3TLMUgP017129@dev.open-bio.org> senger Sat Apr 29 17:22:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv17062/xmls Modified Files: samplesBuild.xml Log Message: add caller address to BaseService moby-live/Java/xmls samplesBuild.xml,1.1,1.2 From senger at dev.open-bio.org Sat Apr 29 21:22:30 2006 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 29 Apr 2006 17:22:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200604292122.k3TLMUi3017110@dev.open-bio.org> senger Sat Apr 29 17:22:30 EDT 2006 Update of /home/repository/moby/moby-live/Java/src/samples/org/jmoby/tutorial/service In directory dev.open-bio.org:/tmp/cvs-serv17062/src/samples/org/jmoby/tutorial/service Modified Files: HelloBiomobyWorldImpl.java Log Message: add caller address to BaseService moby-live/Java/src/samples/org/jmoby/tutorial/service HelloBiomobyWorldImpl.java,1.4,1.5 From llj at dev.open-bio.org Sat Apr 29 00:39:07 2006 From: llj at dev.open-bio.org (Linda Julien) Date: Sat, 29 Apr 2006 00:39:07 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200604290039.k3T0d4Zf015321@dev.open-bio.org> llj Fri Apr 28 20:39:03 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv15201 Modified Files: footer.jsp Added Files: login.jsp Log Message: Added login functionality for things in the /admin directory. NOTE: In order to use this, you'll need to add a 'smoby_admin' user to the tomcat-users.xml file in your tomcat/conf directory, and a role 'smoby_admin'. You can choose the password. There's now a logout link in the footer, as well. s-moby/ref-impl/semanticmoby.org/WebRoot login.jsp,NONE,1.1 footer.jsp,1.9,1.10 From llj at dev.open-bio.org Sat Apr 29 00:39:07 2006 From: llj at dev.open-bio.org (Linda Julien) Date: Sat, 29 Apr 2006 00:39:07 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200604290039.k3T0d4j7015336@dev.open-bio.org> llj Fri Apr 28 20:39:03 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/WEB-INF In directory dev.open-bio.org:/tmp/cvs-serv15201/WEB-INF Modified Files: web.xml Log Message: Added login functionality for things in the /admin directory. NOTE: In order to use this, you'll need to add a 'smoby_admin' user to the tomcat-users.xml file in your tomcat/conf directory, and a role 'smoby_admin'. You can choose the password. There's now a logout link in the footer, as well. s-moby/ref-impl/semanticmoby.org/WebRoot/WEB-INF web.xml,1.13,1.14 From llj at dev.open-bio.org Sat Apr 29 00:39:17 2006 From: llj at dev.open-bio.org (Linda Julien) Date: Sat, 29 Apr 2006 00:39:17 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200604290039.k3T0d48R015366@dev.open-bio.org> llj Fri Apr 28 20:39:03 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/css In directory dev.open-bio.org:/tmp/cvs-serv15201/css Modified Files: smoby.css Log Message: Added login functionality for things in the /admin directory. NOTE: In order to use this, you'll need to add a 'smoby_admin' user to the tomcat-users.xml file in your tomcat/conf directory, and a role 'smoby_admin'. You can choose the password. There's now a logout link in the footer, as well. s-moby/ref-impl/semanticmoby.org/WebRoot/css smoby.css,1.6,1.7 From llj at dev.open-bio.org Sat Apr 29 00:39:17 2006 From: llj at dev.open-bio.org (Linda Julien) Date: Sat, 29 Apr 2006 00:39:17 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200604290039.k3T0d4wa015351@dev.open-bio.org> llj Fri Apr 28 20:39:03 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot/admin In directory dev.open-bio.org:/tmp/cvs-serv15201/admin Modified Files: index.jsp Log Message: Added login functionality for things in the /admin directory. NOTE: In order to use this, you'll need to add a 'smoby_admin' user to the tomcat-users.xml file in your tomcat/conf directory, and a role 'smoby_admin'. You can choose the password. There's now a logout link in the footer, as well. s-moby/ref-impl/semanticmoby.org/WebRoot/admin index.jsp,1.1,1.2 From llj at dev.open-bio.org Sat Apr 29 01:08:06 2006 From: llj at dev.open-bio.org (Linda Julien) Date: Sat, 29 Apr 2006 01:08:06 -0000 Subject: [MOBY-guts] biomoby commit Message-ID: <200604290108.k3T185me015630@dev.open-bio.org> llj Fri Apr 28 21:08:05 EDT 2006 Update of /home/repository/moby/s-moby/ref-impl/semanticmoby.org/WebRoot In directory dev.open-bio.org:/tmp/cvs-serv15574 Modified Files: about.jsp contact.jsp footer.jsp header.jsp index.jsp Log Message: Brought these pages just a little bit closer to valid html. This includes: - don't end and in the header - don't start and in the footer - if a page includeds the header and footer, you don't need to start and end your own html (and, in fact, shouldn't) s-moby/ref-impl/semanticmoby.org/WebRoot about.jsp,1.6,1.7 contact.jsp,1.6,1.7 footer.jsp,1.10,1.11 header.jsp,1.14,1.15 index.jsp,1.10,1.11